Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 50 of 113
Found at i:13120303 original size:13 final size:13
Alignment explanation
Indices: 13120285--13120309 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13120275 TAGAATATTG
13120285 ATCGAATTTACTA
1 ATCGAATTTACTA
13120298 ATCGAATTTACT
1 ATCGAATTTACT
13120310 CCGTAAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (13 bp):
ATCGAATTTACTA
Found at i:13128748 original size:16 final size:17
Alignment explanation
Indices: 13128719--13128751 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
13128709 ATTTAATATT
13128719 AAAAAAATCCAAGAAAAG
1 AAAAAAAT-CAAGAAAAG
13128737 AAAAAAAT-AAGAAAA
1 AAAAAAATCAAGAAAA
13128752 AAGAATAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.79, C:0.06, G:0.09, T:0.06
Consensus pattern (17 bp):
AAAAAAATCAAGAAAAG
Found at i:13128882 original size:60 final size:59
Alignment explanation
Indices: 13128807--13129004 Score: 256
Period size: 60 Copynumber: 3.3 Consensus size: 59
13128797 AATATGAAAG
13128807 TTTTTATTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTGAA
1 TTTTTATTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTGAA
* * *
13128866 TTTTTATTTTTAAGGAAAACTAATAC-TTCTAACTTTCCCTCAAAAATATTTTTTTTTGAAA
1 TTTTTA-TTTTAAGGAAAATTGATACTTTC-AACTTTTCCTCAAAAATATTTTTTTTTG-AA
** ** * * *
13128927 AATTTATTTTTAAAAAAAATTGATACTTTCAATTTTTCCTCAAAAATATATTTTTTAGAA
1 TTTTTA-TTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTGAA
13128987 TTTTTATTTTAA-GAAAAT
1 TTTTTATTTTAAGGAAAAT
13129005 AATTAAAAAA
Statistics
Matches: 119, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
58 5 0.04
59 15 0.13
60 50 0.42
61 46 0.39
62 3 0.03
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (59 bp):
TTTTTATTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTGAA
Found at i:13129056 original size:4 final size:4
Alignment explanation
Indices: 13129047--13129078 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
13129037 ATTCTAATCT
13129047 AATA AATA AAT- AAT- AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AA
13129079 ATGAAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 6 0.22
4 21 0.78
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:13129063 original size:14 final size:14
Alignment explanation
Indices: 13129046--13129073 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13129036 AATTCTAATC
13129046 TAATAAATAAATAA
1 TAATAAATAAATAA
13129060 TAATAAATAAATAA
1 TAATAAATAAATAA
13129074 ATAAAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TAATAAATAAATAA
Found at i:13129974 original size:22 final size:22
Alignment explanation
Indices: 13129946--13130016 Score: 83
Period size: 22 Copynumber: 3.2 Consensus size: 22
13129936 ATAGATATAT
*
13129946 TAATAGATAACTAAAAGAA-AA
1 TAATAGATAAATAAAAGAATAA
*
13129967 TAATTAGATAAATAAAA-AATAT
1 TAA-TAGATAAATAAAAGAATAA
13129989 TAATAGATAAATAATAAGAATAA
1 TAATAGATAAATAA-AAGAATAA
*
13130012 GAATA
1 TAATA
13130017 ATGAAAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
21 16 0.38
22 18 0.43
23 8 0.19
ACGTcount: A:0.65, C:0.01, G:0.08, T:0.25
Consensus pattern (22 bp):
TAATAGATAAATAAAAGAATAA
Found at i:13129998 original size:17 final size:18
Alignment explanation
Indices: 13129963--13130004 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
13129953 TAACTAAAAG
13129963 AAAATAATTAGATAAATAA
1 AAAAT-ATTAGATAAATAA
*
13129982 AAAATATTA-ATAGATAA
1 AAAATATTAGATAAATAA
*
13129999 ATAATA
1 AAAATA
13130005 AGAATAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 12 0.57
18 4 0.19
19 5 0.24
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (18 bp):
AAAATATTAGATAAATAA
Found at i:13130221 original size:11 final size:11
Alignment explanation
Indices: 13130205--13130234 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
13130195 CAACTTGACA
13130205 TTTTTTTTGCT
1 TTTTTTTTGCT
13130216 TTTTTTTT-CT
1 TTTTTTTTGCT
13130226 TTTTTTTTG
1 TTTTTTTTG
13130235 GTTAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.87
Consensus pattern (11 bp):
TTTTTTTTGCT
Found at i:13130303 original size:44 final size:41
Alignment explanation
Indices: 13130250--13130582 Score: 275
Period size: 44 Copynumber: 7.9 Consensus size: 41
13130240 AATTTTGATC
13130250 AAAGCTCCTCTAAGTAGAGGCTCAACGACTTTGATAAAATAAA
1 AAAGCTCCTCTAA-TAGAGGCTCAACGACTTTGA-AAAATAAA
* *
13130293 CAAAGCTCCTCTAAACAGAGGCTCCACGAC-TTG-AAAAT-AA
1 -AAAGCTCCTCT-AATAGAGGCTCAACGACTTTGAAAAATAAA
** * * * *
13130333 ATGGTTCCTCTAATCAGAGGTTCAATGACTTTGGAAAAT-AA
1 AAAGCTCCTCTAAT-AGAGGCTCAACGACTTTGAAAAATAAA
** * *
13130374 ATGGCTCCCCTAATCAGAGGCTCAACGACTTTGGAAAAT-AA
1 AAAGCTCCTCTAAT-AGAGGCTCAACGACTTTGAAAAATAAA
** * *
13130415 ATGGCTCCTTTAATCAGAGGCTCAACAACTTTTGAAAAAATAAA
1 AAAGCTCCTCTAAT-AGAGGCTCAACGAC-TTTG-AAAAATAAA
*
13130459 TAAAGCTCCTCTAAACAGAGGCTCAACGACTTTTGAAAAATAAA
1 -AAAGCTCCTCT-AATAGAGGCTCAACGAC-TTTGAAAAATAAA
* *
13130503 CAAAGCTCCTCTAAACAGAGGCTCAACAACTTTGAAAAAATAAA
1 -AAAGCTCCTCT-AATAGAGGCTCAACGACTTTG-AAAAATAAA
*
13130547 TAAAGCT-CTCTAATTAGAGGCATC-ACAACTTTGAAA
1 -AAAGCTCCTCTAA-TAGAGGC-TCAACGACTTTGAAA
13130583 GTAAATGCTC
Statistics
Matches: 251, Mismatches: 26, Indels: 26
0.83 0.09 0.09
Matches are distributed among these distances:
38 2 0.01
39 19 0.08
40 5 0.02
41 75 0.30
42 9 0.04
43 31 0.12
44 80 0.32
45 28 0.11
46 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (41 bp):
AAAGCTCCTCTAATAGAGGCTCAACGACTTTGAAAAATAAA
Found at i:13130370 original size:41 final size:41
Alignment explanation
Indices: 13130253--13130589 Score: 281
Period size: 41 Copynumber: 8.0 Consensus size: 41
13130243 TTTGATCAAA
* **
13130253 GCTCCTCTAAGT-AGAGGCTCAACGACTTTGATAAAATAAACAAA
1 GCTCCTCTAA-TCAGAGGCTCAACGACTTTG-GAAAAT-AA-ATG
* *
13130297 GCTCCTCTAAACAGAGGCTCCACGAC-TT-GAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGGAAAATAAATG
* * *
13130336 GTTCCTCTAATCAGAGGTTCAATGACTTTGGAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGGAAAATAAATG
*
13130377 GCTCCCCTAATCAGAGGCTCAACGACTTTGGAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGGAAAATAAATG
* * * *
13130418 GCTCCTTTAATCAGAGGCTCAACAACTTTTGAAAAAATAAATAAA
1 GCTCCTCTAATCAGAGGCTCAACGAC-TTTG-GAAAATAAAT--G
* * **
13130463 GCTCCTCTAAACAGAGGCTCAACGACTTTTGAAAAATAAACAAA
1 GCTCCTCTAATCAGAGGCTCAACGAC-TTTGGAAAAT-AA-ATG
* * * *
13130507 GCTCCTCTAAACAGAGGCTCAACAACTTTGAAAAAATAAATAAA
1 GCTCCTCTAATCAGAGGCTCAACGACTTTG-GAAAATAAAT--G
* * *
13130551 GCT-CTCTAATTAGAGGCATC-ACAACTTT-GAAAGTAAATG
1 GCTCCTCTAATCAGAGGC-TCAACGACTTTGGAAAATAAATG
13130590 CTCATTGACA
Statistics
Matches: 250, Mismatches: 30, Indels: 31
0.80 0.10 0.10
Matches are distributed among these distances:
39 22 0.09
40 4 0.02
41 84 0.34
42 5 0.02
43 37 0.15
44 67 0.27
45 30 0.12
46 1 0.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAATCAGAGGCTCAACGACTTTGGAAAATAAATG
Found at i:13130429 original size:82 final size:85
Alignment explanation
Indices: 13130253--13130589 Score: 336
Period size: 82 Copynumber: 4.0 Consensus size: 85
13130243 TTTGATCAAA
* * *
13130253 GCTCCTCTAAGT-AGAGGCTCAACGAC-TTTGATAAAATAAACAAAGCTCCTCTAAACAGAGGCT
1 GCTCCTCTAA-TCAGAGGCTCAACAACTTTTGAAAAAATAAA-TAAGCTCCTCTAAACAGAGGCT
*
13130316 CCACGAC-TT-GAAAATAAATG
64 CAACGACTTTGGAAAATAAATG
* * ** * * * *
13130336 GTTCCTCTAATCAGAGGTTCAATGAC-TTTG-GAAAATAAAT-GGCTCCCCTAATCAGAGGCTCA
1 GCTCCTCTAATCAGAGGCTCAACAACTTTTGAAAAAATAAATAAGCTCCTCTAAACAGAGGCTCA
13130398 ACGACTTTGGAAAATAAATG
66 ACGACTTTGGAAAATAAATG
*
13130418 GCTCCTTTAATCAGAGGCTCAACAACTTTTGAAAAAATAAATAAAGCTCCTCTAAACAGAGGCTC
1 GCTCCTCTAATCAGAGGCTCAACAACTTTTGAAAAAATAAAT-AAGCTCCTCTAAACAGAGGCTC
* **
13130483 AACGACTTTTGAAAAATAAACAAA
65 AACGAC-TTTGGAAAAT-AA-ATG
* **
13130507 GCTCCTCTAAACAGAGGCTCAACAAC-TTTGAAAAAATAAATAAAGCT-CTCTAATTAGAGGCAT
1 GCTCCTCTAATCAGAGGCTCAACAACTTTTGAAAAAATAAAT-AAGCTCCTCTAAACAGAGGC-T
* *
13130570 C-ACAACTTT-GAAAGTAAATG
64 CAACGACTTTGGAAAATAAATG
13130590 CTCATTGACA
Statistics
Matches: 213, Mismatches: 30, Indels: 22
0.80 0.11 0.08
Matches are distributed among these distances:
80 23 0.11
81 2 0.01
82 41 0.19
83 30 0.14
84 11 0.05
85 4 0.02
86 27 0.13
87 25 0.12
88 25 0.12
89 25 0.12
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (85 bp):
GCTCCTCTAATCAGAGGCTCAACAACTTTTGAAAAAATAAATAAGCTCCTCTAAACAGAGGCTCA
ACGACTTTGGAAAATAAATG
Found at i:13130725 original size:30 final size:30
Alignment explanation
Indices: 13130691--13130752 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
13130681 ATCGAGAGAT
13130691 ATCCTATTTCAAGGATTAGAAACTTACTTG
1 ATCCTATTTCAAGGATTAGAAACTTACTTG
13130721 ATCCTATTTCAAGGATTAGAAACTTACTTG
1 ATCCTATTTCAAGGATTAGAAACTTACTTG
13130751 AT
1 AT
13130753 AAGATTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (30 bp):
ATCCTATTTCAAGGATTAGAAACTTACTTG
Found at i:13132799 original size:22 final size:21
Alignment explanation
Indices: 13132774--13132818 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
13132764 TAAAAAAGAT
*
13132774 AAATATATTA-ATAGATAACAAA
1 AAATA-ATTAGATAAATAA-AAA
13132796 AAATAATTAGATAAATAAAAA
1 AAATAATTAGATAAATAAAAA
13132817 AA
1 AA
13132819 CAAATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (21 bp):
AAATAATTAGATAAATAAAAA
Found at i:13132904 original size:34 final size:38
Alignment explanation
Indices: 13132858--13132939 Score: 127
Period size: 34 Copynumber: 2.3 Consensus size: 38
13132848 GCAGATAAAT
*
13132858 AATAAAAATATTAATAGATA-A-AAA-AATAAAAATAA
1 AATAAAAATATTAATAAATAGATAAATAATAAAAATAA
13132893 AA-AAAAATATTAATAAATAGATAAATAATAAAAATAA
1 AATAAAAATATTAATAAATAGATAAATAATAAAAATAA
13132930 AATAAAAATA
1 AATAAAAATA
13132940 AAAATAAAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
34 16 0.38
35 3 0.07
36 3 0.07
37 13 0.31
38 7 0.17
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (38 bp):
AATAAAAATATTAATAAATAGATAAATAATAAAAATAA
Found at i:13132937 original size:38 final size:35
Alignment explanation
Indices: 13132794--13132939 Score: 124
Period size: 33 Copynumber: 4.2 Consensus size: 35
13132784 ATAGATAACA
*
13132794 AAAAATAATTAGATAAAT-AAAAAA-ACAAAT-AAAT
1 AAAAAT-ATTA-ATAAATAAAAAAATAAAAATAAAAT
* * * ** * *
13132828 AATAATAATAAGAAATAAAAGCAGATAAAT--AAT
1 AAAAATATTAATAAATAAAAAAATAAAAATAAAAT
*
13132861 AAAAATATTAATAGATAAAAAAATAAAAATAAAA-
1 AAAAATATTAATAAATAAAAAAATAAAAATAAAAT
13132895 AAAAATATTAATAAATAGATAAATAATAAAAATAAAAT
1 AAAAATATTAATAAATA-A-AAA-AATAAAAATAAAAT
13132933 AAAAATA
1 AAAAATA
13132940 AAAATAAAAG
Statistics
Matches: 89, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
32 5 0.06
33 32 0.36
34 26 0.29
35 3 0.03
36 3 0.03
37 13 0.15
38 7 0.08
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.22
Consensus pattern (35 bp):
AAAAATATTAATAAATAAAAAAATAAAAATAAAAT
Found at i:13132945 original size:34 final size:34
Alignment explanation
Indices: 13132760--13132945 Score: 109
Period size: 37 Copynumber: 5.4 Consensus size: 34
13132750 AAAATTAATC
* *
13132760 AAAATAAAAA-AGATAAATATATTAATAGATAACA-A
1 AAAATAAAAATAGATAAATA-A-TAA-AAATAAAATA
* *
13132795 AAAAT--AATTAGATAAATAA-AAAAA-CAAATA
1 AAAATAAAAATAGATAAATAATAAAAATAAAATA
* * *
13132825 AATAATAATAATA-AGAAATAA-AAGCAGATAAATAATA
1 AA-AATAAAAATAGATAAATAATAA--AAAT-AA-AATA
** * *
13132862 AAAATATTAATAGATAAAAAAATAAAAATAAAAAA
1 AAAATAAAAATAGAT-AAATAATAAAAATAAAATA
13132897 AAATATTAATAAATAGATAAATAATAAAAATAAAATA
1 AAA-A-TAA-AAATAGATAAATAATAAAAATAAAATA
13132934 AAAATAAAAATA
1 AAAATAAAAATA
13132946 AAAGCCAATT
Statistics
Matches: 117, Mismatches: 18, Indels: 33
0.70 0.11 0.20
Matches are distributed among these distances:
29 2 0.02
30 5 0.04
31 5 0.04
32 9 0.08
33 6 0.05
34 16 0.14
35 14 0.12
36 14 0.12
37 32 0.27
38 12 0.10
39 2 0.02
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.22
Consensus pattern (34 bp):
AAAATAAAAATAGATAAATAATAAAAATAAAATA
Found at i:13132946 original size:38 final size:39
Alignment explanation
Indices: 13132852--13132947 Score: 124
Period size: 38 Copynumber: 2.4 Consensus size: 39
13132842 ATAAAAGCAG
13132852 ATAAATAATAAAAATATTAATAGATAAAAAAATAAAAATAAA
1 ATAAA-AATAAAAATA--AATAGATAAAAAAATAAAAATAAA
** *
13132894 A-AAAAATATTAATAAATAGAT-AAATAATAAAAATAAA
1 ATAAAAATAAAAATAAATAGATAAAAAAATAAAAATAAA
13132931 ATAAAAATAAAAATAAA
1 ATAAAAATAAAAATAAA
13132948 AGCCAATTGG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
37 16 0.33
38 20 0.42
40 8 0.17
41 3 0.06
42 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (39 bp):
ATAAAAATAAAAATAAATAGATAAAAAAATAAAAATAAA
Found at i:13132947 original size:6 final size:6
Alignment explanation
Indices: 13132808--13132948 Score: 85
Period size: 6 Copynumber: 22.3 Consensus size: 6
13132798 ATAATTAGAT
*
13132808 AAATAA AAA-AA CAAATAA ATAATAA TAATAA GAAATAAA AGCAGATAA
1 AAATAA AAATAA -AAATAA A-AATAA AAATAA -AAAT-AA A--A-ATAA
* * * *
13132856 ATAATAA AAATAT TAATAGA TAA-AA AAATAA AAAT-A AAA-AA AAATAT
1 A-AATAA AAATAA AAATA-A AAATAA AAATAA AAATAA AAATAA AAATAA
*
13132903 TAATAA ATAGATAA ATAATAA AAAT-A AAATAA AAATAA AAATAA AA
1 AAATAA A-A-ATAA A-AATAA AAATAA AAATAA AAATAA AAATAA AA
13132949 GCCAATTGGG
Statistics
Matches: 109, Mismatches: 11, Indels: 30
0.73 0.07 0.20
Matches are distributed among these distances:
5 18 0.17
6 50 0.46
7 25 0.23
8 10 0.09
9 4 0.04
10 2 0.02
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (6 bp):
AAATAA
Found at i:13132947 original size:30 final size:29
Alignment explanation
Indices: 13132808--13132947 Score: 106
Period size: 30 Copynumber: 4.6 Consensus size: 29
13132798 ATAATTAGAT
*
13132808 AAATAAAAAAACAAATAAATAATAATAATA
1 AAATAAAAAAA-AAATAAATAATAAAAATA
** *
13132838 AGAA-ATAAAAGCAGATAAATAATAAAAATA
1 A-AATA-AAAAAAAAATAAATAATAAAAATA
* *
13132868 TTAATAGATAAAAAAATAAA-AATAAAAA-A
1 -AAATA-AAAAAAAAATAAATAATAAAAATA
* *
13132897 AAATATTAATAAATAGATAAATAATAAAAATA
1 AAATA--AA-AAAAAAATAAATAATAAAAATA
13132929 AAATAAAAATAAAAATAAA
1 AAATAAAAA-AAAAATAAA
13132948 AGCCAATTGG
Statistics
Matches: 84, Mismatches: 17, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
28 4 0.05
29 4 0.05
30 46 0.55
31 24 0.29
32 6 0.07
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (29 bp):
AAATAAAAAAAAAATAAATAATAAAAATA
Found at i:13133567 original size:15 final size:16
Alignment explanation
Indices: 13133525--13133567 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
13133515 TCTTGAATCC
*
13133525 ATTCAGCTTC-TTCAA
1 ATTCAACTTCTTTCAA
13133540 ATTCAACTTCTTTC-A
1 ATTCAACTTCTTTCAA
13133555 ATTCAACTTCTTT
1 ATTCAACTTCTTT
13133568 TAGAACTCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 23 0.88
16 3 0.12
ACGTcount: A:0.26, C:0.26, G:0.02, T:0.47
Consensus pattern (16 bp):
ATTCAACTTCTTTCAA
Found at i:13148632 original size:59 final size:61
Alignment explanation
Indices: 13148559--13148807 Score: 339
Period size: 59 Copynumber: 4.2 Consensus size: 61
13148549 AAGTTTTTAA
* *
13148559 TTTAAGGAAAATTGATATTTTCAACTTTTCCTCAAAAATAT-TTTTTTTGAAATTTTTATT
1 TTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATATTTTTTTGAAATTTTTATT
* * * * *
13148619 TTTTA-AAAAATTGATACTTTCAACTCTTCCCCGAAAATATATTTTTTTGGAATTTTTATT
1 TTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATATTTTTTTGAAATTTTTATT
* * *
13148679 TTTAAGAAAAATTGATACTTTCAACTTTCCCTCAAAAATAT-TTTTTTAGAAA-TTTTATC
1 TTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATATTTTTTTGAAATTTTTATT
* *
13148738 TTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATATTTTTTT-AGAATTTTTA-T
1 TTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATATTTTTTTGA-AATTTTTATT
13148798 TTTAAGAAAA
1 TTTAAGAAAA
13148808 TCATTAAAAA
Statistics
Matches: 163, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
59 75 0.46
60 52 0.32
61 36 0.22
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (61 bp):
TTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATATTTTTTTGAAATTTTTATT
Found at i:13148690 original size:120 final size:119
Alignment explanation
Indices: 13148546--13148807 Score: 373
Period size: 120 Copynumber: 2.2 Consensus size: 119
13148536 AAAAAAAACA
* * * * *
13148546 TGGAAGTTTTTAATTTAAGGAAAATTGATATTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAA
1 TGGAA-TTTTTATTTTAAGAAAAATTGATACTTTCAACTTTCCCTCAAAAATATTTTTTTAGAAA
* ** *
13148611 TTTTTATTTTTTA-AAAAATTGATACTTTCAACTCTTCCCCGAAAATATATTTTTT
65 -TTTTATCTTCAAGAAAAATTGATACTTTCAACTCTTCCCCAAAAATATATTTTTT
13148666 TGGAATTTTTATTTTTAAGAAAAATTGATACTTTCAACTTTCCCTCAAAAATATTTTTTTAGAAA
1 TGGAATTTTTA-TTTTAAGAAAAATTGATACTTTCAACTTTCCCTCAAAAATATTTTTTTAGAAA
* **
13148731 TTTTATCTTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATATTTTTT
65 TTTTATCTTCAAGAAAAATTGATACTTTCAACTCTTCCCCAAAAATATATTTTTT
*
13148786 TAGAATTTTTATTTTAAGAAAA
1 TGGAATTTTTATTTTAAGAAAA
13148808 TCATTAAAAA
Statistics
Matches: 127, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
119 26 0.20
120 101 0.80
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47
Consensus pattern (119 bp):
TGGAATTTTTATTTTAAGAAAAATTGATACTTTCAACTTTCCCTCAAAAATATTTTTTTAGAAAT
TTTATCTTCAAGAAAAATTGATACTTTCAACTCTTCCCCAAAAATATATTTTTT
Found at i:13148863 original size:19 final size:18
Alignment explanation
Indices: 13148812--13148855 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
13148802 AGAAAATCAT
13148812 TAAAAA-AATAAATAAATA
1 TAAAAATAA-AAATAAATA
13148830 TAAAAATAAAAATAAA-A
1 TAAAAATAAAAATAAATA
13148847 TAAGAAATA
1 TAA-AAATA
13148856 CCAAATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.17
18 18 0.75
19 2 0.08
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (18 bp):
TAAAAATAAAAATAAATA
Found at i:13149799 original size:21 final size:23
Alignment explanation
Indices: 13149775--13149867 Score: 90
Period size: 22 Copynumber: 4.2 Consensus size: 23
13149765 ATAGATATAT
*
13149775 TAATAGATAACTAA-AAGAA-AA
1 TAATAGATAAATAATAAGAATAA
*
13149796 TAATTAGATAAATAA-AA-AATAT
1 TAA-TAGATAAATAATAAGAATAA
*
13149818 TAATAGATAAATAATAATAATAA
1 TAATAGATAAATAATAAGAATAA
*
13149841 TAATA-AT-AATAATAATGAAAAA
1 TAATAGATAAATAATAA-GAATAA
13149863 TAATA
1 TAATA
13149868 AAATTAAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
21 24 0.39
22 29 0.47
23 9 0.15
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.28
Consensus pattern (23 bp):
TAATAGATAAATAATAAGAATAA
Found at i:13149835 original size:3 final size:3
Alignment explanation
Indices: 13149813--13149868 Score: 67
Period size: 3 Copynumber: 17.7 Consensus size: 3
13149803 ATAAATAAAA
* *
13149813 AAT ATT AAT AGAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAAA
1 AAT AAT AAT A-AT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
13149861 AAT AAT AA
1 AAT AAT AA
13149869 AATTAAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
3 39 0.85
4 6 0.13
5 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:13150437 original size:30 final size:31
Alignment explanation
Indices: 13150398--13150462 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
13150388 TGAAATTATT
* * *
13150398 TTTTGAAAAATTTTTTG-AAACATTTAAAAAA
1 TTTTGAAAAAATTATTGCAAA-ATTAAAAAAA
13150429 TTTT-AAAAAATTATTGCAAAATTAAAAAAA
1 TTTTGAAAAAATTATTGCAAAATTAAAAAAA
13150459 TTTT
1 TTTT
13150463 CAAACATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 23 0.77
31 7 0.23
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.42
Consensus pattern (31 bp):
TTTTGAAAAAATTATTGCAAAATTAAAAAAA
Found at i:13150474 original size:19 final size:20
Alignment explanation
Indices: 13150433--13150474 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
13150423 AAAAAATTTT
*
13150433 AAAAAATTATTGCAAAATTA
1 AAAAAATTATTGCAAAATAA
13150453 AAAAAATT-TT-CAAACATAA
1 AAAAAATTATTGCAAA-ATAA
13150472 AAA
1 AAA
13150475 GTTGAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 4 0.20
19 8 0.40
20 8 0.40
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAAAATTATTGCAAAATAA
Found at i:13150595 original size:11 final size:10
Alignment explanation
Indices: 13150577--13150622 Score: 65
Period size: 11 Copynumber: 4.4 Consensus size: 10
13150567 TTTTTTTTAA
*
13150577 TTTTAAAAAT
1 TTTTCAAAAT
13150587 TTTTCAAAAAT
1 TTTTC-AAAAT
13150598 TTTTCAAAAT
1 TTTTCAAAAT
13150608 TATTTCAAAAT
1 T-TTTCAAAAT
13150619 TTTT
1 TTTT
13150623 AGATTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
10 13 0.39
11 20 0.61
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (10 bp):
TTTTCAAAAT
Found at i:13150601 original size:21 final size:21
Alignment explanation
Indices: 13150577--13150623 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
13150567 TTTTTTTTAA
13150577 TTTTAAAAATT-TTTCAAAAAT
1 TTTTAAAAATTATTTC-AAAAT
*
13150598 TTTTCAAAATTATTTCAAAAT
1 TTTTAAAAATTATTTCAAAAT
13150619 TTTTA
1 TTTTA
13150624 GATTTTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTAAAAATTATTTCAAAAT
Found at i:13151290 original size:21 final size:20
Alignment explanation
Indices: 13151252--13151290 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
13151242 TTGATTTTTT
*
13151252 AAAAAAATTATTATCGATGA
1 AAAAAAATTATTACCGATGA
*
13151272 AAAAAATATTTTTACCGAT
1 AAAAAA-ATTATTACCGAT
13151291 AGAATATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (20 bp):
AAAAAAATTATTACCGATGA
Found at i:13151934 original size:16 final size:15
Alignment explanation
Indices: 13151913--13151951 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
13151903 TATTTGAAAA
*
13151913 TTTATTTTGTTTTAAT
1 TTTATTTTATTTT-AT
13151929 TTTATTTTATTTTAT
1 TTTATTTTATTTTAT
13151944 TTTATTTT
1 TTTATTTT
13151952 TAATTTATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTATTTTATTTTAT
Found at i:13151935 original size:5 final size:5
Alignment explanation
Indices: 13151913--13151951 Score: 60
Period size: 5 Copynumber: 7.6 Consensus size: 5
13151903 TATTTGAAAA
*
13151913 TTTAT TTTGT TTTAAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTT-AT TTTAT TTTAT TTTAT TTTAT TTT
13151952 TAATTTATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:13151936 original size:11 final size:11
Alignment explanation
Indices: 13151916--13151958 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
13151906 TTGAAAATTT
*
13151916 ATTTTGTTTTA
1 ATTTTATTTTA
13151927 ATTTTATTTT-
1 ATTTTATTTTA
13151937 ATTTTATTTTA
1 ATTTTATTTTA
* *
13151948 TTTTTAATTTA
1 ATTTTATTTTA
13151959 TTGAATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 10 0.36
11 18 0.64
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (11 bp):
ATTTTATTTTA
Found at i:13151939 original size:21 final size:21
Alignment explanation
Indices: 13151911--13151960 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
13151901 TGTATTTGAA
*
13151911 AATTTATTTTGTTTTAATTTT
1 AATTTATTTTATTTTAATTTT
* *
13151932 ATTTTATTTTATTTTATTTTT
1 AATTTATTTTATTTTAATTTT
13151953 AATTTATT
1 AATTTATT
13151961 GAATTTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (21 bp):
AATTTATTTTATTTTAATTTT
Found at i:13151952 original size:16 final size:16
Alignment explanation
Indices: 13151913--13151960 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
13151903 TATTTGAAAA
*
13151913 TTTATTTTGT-TTTAAT
1 TTTATTTT-TATTTTAT
13151929 TTTA-TTTTATTTTAT
1 TTTATTTTTATTTTAT
*
13151944 TTTATTTTTAATTTAT
1 TTTATTTTTATTTTAT
13151960 T
1 T
13151961 GAATTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 1 0.04
15 12 0.43
16 15 0.54
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTATTTTTATTTTAT
Found at i:13151966 original size:21 final size:21
Alignment explanation
Indices: 13151922--13151966 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
13151912 ATTTATTTTG
* **
13151922 TTTTAATTTTATTTTATTTTA
1 TTTTAATTTTAATTTATTGAA
*
13151943 TTTTATTTTTAATTTATTGAA
1 TTTTAATTTTAATTTATTGAA
13151964 TTT
1 TTT
13151967 AAAAACATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTAATTTTAATTTATTGAA
Found at i:13154729 original size:20 final size:21
Alignment explanation
Indices: 13154693--13154744 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
13154683 TCCGAAATTA
13154693 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
*
13154715 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTAAAAT
13154736 AT-AAATATT
1 ATAAAATATT
13154745 TAAAAATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 11 0.38
22 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:13154735 original size:21 final size:22
Alignment explanation
Indices: 13154693--13154744 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
13154683 TCCGAAATTA
13154693 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
13154715 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
13154736 AT-AAATATT
1 ATAAAATATT
13154745 TAAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:13154752 original size:30 final size:30
Alignment explanation
Indices: 13154717--13154773 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
13154707 TTTAAAATAT
* * *
13154717 AAAATATTATTTTTTAAATATAAATATTTA
1 AAAATATCATTATATAAATATAAATATTTA
*
13154747 AAAATATCATTATATAAATATATATAT
1 AAAATATCATTATATAAATATAAATAT
13154774 AATTAATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (30 bp):
AAAATATCATTATATAAATATAAATATTTA
Found at i:13156690 original size:2 final size:2
Alignment explanation
Indices: 13156683--13156717 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
13156673 CTCATCTTAC
13156683 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13156718 GTCGGTCCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13157272 original size:32 final size:32
Alignment explanation
Indices: 13157206--13157285 Score: 99
Period size: 33 Copynumber: 2.5 Consensus size: 32
13157196 TATACCATTT
* *
13157206 TTAAAATTTTAAATTAAATTATTTTATAGTAA
1 TTAAAATTTTAAATTTAATAATTTTATAGTAA
*
13157238 TTAAAATTATTAAATTTAATAATTTTATTG-AA
1 TTAAAATT-TTAAATTTAATAATTTTATAGTAA
* *
13157270 TTATAATTTTACATTT
1 TTAAAATTTTAAATTT
13157286 TTATTCTTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
31 7 0.17
32 17 0.40
33 18 0.43
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (32 bp):
TTAAAATTTTAAATTTAATAATTTTATAGTAA
Found at i:13166353 original size:17 final size:17
Alignment explanation
Indices: 13166323--13166357 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
13166313 ATAAAGTTGT
*
13166323 GAAAATAAAAAAAAAAA
1 GAAAAGAAAAAAAAAAA
13166340 GAAAAGAAAGAAAAAAAA
1 GAAAAGAAA-AAAAAAAA
13166358 ACTTTGAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (17 bp):
GAAAAGAAAAAAAAAAA
Found at i:13172541 original size:30 final size:30
Alignment explanation
Indices: 13172507--13172567 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
13172497 TTTGCTTGTT
*
13172507 TGCTTGCTATAGCAGTTTGGTTTGCCTACA
1 TGCTTGCTATAGCAGTTTGGTTTACCTACA
* * **
13172537 TGCTTGTTGTTTCAGTTTGGTTTACCTACA
1 TGCTTGCTATAGCAGTTTGGTTTACCTACA
13172567 T
1 T
13172568 ATGTTAGTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.46
Consensus pattern (30 bp):
TGCTTGCTATAGCAGTTTGGTTTACCTACA
Found at i:13172583 original size:32 final size:31
Alignment explanation
Indices: 13172519--13172612 Score: 120
Period size: 32 Copynumber: 3.0 Consensus size: 31
13172509 CTTGCTATAG
13172519 CAGTTTGGTTTGCCTAC--ATGCTTGTTGTTT
1 CAGTTTGGTTTGCCTACATATG-TTGTTGTTT
*
13172549 CAGTTTGGTTTACCTACATATGTTAGTTGTTT
1 CAGTTTGGTTTGCCTACATATGTT-GTTGTTT
* *
13172581 CAGGTTGGTTTGCCTACATATATTTGTTGTTT
1 CAGTTTGGTTTGCCTACATAT-GTTGTTGTTT
13172613 GGTTTACTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
30 16 0.29
31 2 0.04
32 36 0.64
33 2 0.04
ACGTcount: A:0.15, C:0.14, G:0.21, T:0.50
Consensus pattern (31 bp):
CAGTTTGGTTTGCCTACATATGTTGTTGTTT
Found at i:13172701 original size:32 final size:32
Alignment explanation
Indices: 13172613--13172732 Score: 82
Period size: 32 Copynumber: 3.8 Consensus size: 32
13172603 TTTGTTGTTT
* * * * *
13172613 GGTTTACTTGTATGTGTTGACTATTTTGATTTG
1 GGTTTACTTGCATATGTTGCCTA-TTTCAATTG
* * *
13172646 AG-TTACCTGCATCTGTT-CACTATTTCAATTG
1 GGTTTACTTGCATATGTTGC-CTATTTCAATTG
* * *** *
13172677 GGTTTACTTGTATATGTTGGCTATTTTGGTTT
1 GGTTTACTTGCATATGTTGCCTATTTCAATTG
13172709 GGTTTACTTGCATATGTTGCCTAT
1 GGTTTACTTGCATATGTTGCCTAT
13172733 CTTGATTCAA
Statistics
Matches: 66, Mismatches: 18, Indels: 7
0.73 0.20 0.08
Matches are distributed among these distances:
31 8 0.12
32 57 0.86
33 1 0.02
ACGTcount: A:0.17, C:0.12, G:0.21, T:0.50
Consensus pattern (32 bp):
GGTTTACTTGCATATGTTGCCTATTTCAATTG
Found at i:13173310 original size:3 final size:3
Alignment explanation
Indices: 13173302--13173354 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
13173292 CTACAAAGAC
13173302 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
13173350 ATA AT
1 ATA AT
13173355 TTTAAAACAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:13175076 original size:12 final size:13
Alignment explanation
Indices: 13175055--13175079 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13175045 TGATATTTAA
13175055 TTTAATTTTTTTT
1 TTTAATTTTTTTT
13175068 TTTAATTTTTTT
1 TTTAATTTTTTT
13175080 AAAAAAATGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTAATTTTTTTT
Found at i:13177070 original size:17 final size:17
Alignment explanation
Indices: 13177044--13177078 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
13177034 TGATGGTTGT
*
13177044 AACAAAAAAAAAGAAAA
1 AACAAAAAAAAACAAAA
*
13177061 AACAACAAAAAACAAAA
1 AACAAAAAAAAACAAAA
13177078 A
1 A
13177079 TGATGAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (17 bp):
AACAAAAAAAAACAAAA
Found at i:13179734 original size:34 final size:34
Alignment explanation
Indices: 13179678--13179976 Score: 212
Period size: 34 Copynumber: 8.9 Consensus size: 34
13179668 TTAATTCCAA
* * *
13179678 TTTAGTTGGCCTTTAAAAAAAGATTTAAGCCCAG
1 TTTAGCTGGCCTTCAAAGAAAGATTTAAGCCCAG
** *
13179712 TTTAAATGGCCCTCAAAGAAAGATTTAAGCCCAG
1 TTTAGCTGGCCTTCAAAGAAAGATTTAAGCCCAG
* * * * * **
13179746 ATTAGCTAG-CTACCAATGAAATA-TTAAGCTTAG
1 TTTAGCTGGCCT-TCAAAGAAAGATTTAAGCCCAG
* * * *
13179779 TTTAGCTAGCATTCAAAGAAATA-TTAAACCCAG
1 TTTAGCTGGCCTTCAAAGAAAGATTTAAGCCCAG
* *
13179812 TTTAGTTGGCCTTCAAAGAAAGATTTAAGCCCAA
1 TTTAGCTGGCCTTCAAAGAAAGATTTAAGCCCAG
* * * * *
13179846 ATTAGATGGCCTTTAAAAAAAGATTTTAGCCCAG
1 TTTAGCTGGCCTTCAAAGAAAGATTTAAGCCCAG
* ** * * * *
13179880 ATTAGCTGGCCACCAATGAAATA-TTAAGCCTAA
1 TTTAGCTGGCCTTCAAAGAAAGATTTAAGCCCAG
* ** *
13179913 TTTTGCTGGCCTTCAAAGAAAGATTTAATTCCAA
1 TTTAGCTGGCCTTCAAAGAAAGATTTAAGCCCAG
* *
13179947 ATTAGTTGGCCTT-AGAAGAAAGATTTAAGC
1 TTTAGCTGGCCTTCA-AAGAAAGATTTAAGC
13179977 ACAAATTAGC
Statistics
Matches: 202, Mismatches: 58, Indels: 10
0.75 0.21 0.04
Matches are distributed among these distances:
33 77 0.38
34 125 0.62
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (34 bp):
TTTAGCTGGCCTTCAAAGAAAGATTTAAGCCCAG
Found at i:13179814 original size:33 final size:32
Alignment explanation
Indices: 13179724--13179844 Score: 107
Period size: 33 Copynumber: 3.6 Consensus size: 32
13179714 TAAATGGCCC
* *
13179724 TCAAAGAAAGATTTAAGCCCAGATTAGCTAGCT
1 TCAAAGAAATA-TTAAGCCCAGTTTAGCTAGCT
* * **
13179757 ACCAATGAAATATTAAGCTTAGTTTAGCTAGCAT
1 -TCAAAGAAATATTAAGCCCAGTTTAGCTAGC-T
* * *
13179791 TCAAAGAAATATTAAACCCAGTTTAGTTGGCCT
1 TCAAAGAAATATTAAGCCCAGTTTAGCTAG-CT
*
13179824 TCAAAGAAAGATTTAAGCCCA
1 TCAAAGAAATA-TTAAGCCCA
13179845 AATTAGATGG
Statistics
Matches: 69, Mismatches: 15, Indels: 6
0.77 0.17 0.07
Matches are distributed among these distances:
33 51 0.74
34 18 0.26
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (32 bp):
TCAAAGAAATATTAAGCCCAGTTTAGCTAGCT
Found at i:13179822 original size:134 final size:134
Alignment explanation
Indices: 13179662--13179984 Score: 423
Period size: 134 Copynumber: 2.4 Consensus size: 134
13179652 GGTCGCCAAT
* **
13179662 GAAATATTAATTCCAATTTAGTTGGCCTTTAAAAAAAGATTTAAGCCCAGTTTAAATGGCCCTCA
1 GAAATATTAATTCCAATTTAGTTGGCCTTTAAAGAAAGATTTAAGCCCAAATTAAATGGCCCTCA
* * * *
13179727 AAGAAAGATTTAAGCCCAGATTAGCTAGCTACCAATGAAATATTAAGCTTAGTTTAGCTAGCATT
66 AAAAAAGATTTAAGCCCAGATTAGCTAGCCACCAATGAAATATTAAGCCTAATTTAGCTAGCATT
13179792 CAAA
131 CAAA
** * * * * *
13179796 GAAATATTAAACCCAGTTTAGTTGGCCTTCAAAGAAAGATTTAAGCCCAAATTAGATGGCCTTTA
1 GAAATATTAATTCCAATTTAGTTGGCCTTTAAAGAAAGATTTAAGCCCAAATTAAATGGCCCTCA
* * * * *
13179861 AAAAAAGATTTTAGCCCAGATTAGCTGGCCACCAATGAAATATTAAGCCTAATTTTGCTGGCCTT
66 AAAAAAGATTTAAGCCCAGATTAGCTAGCCACCAATGAAATATTAAGCCTAATTTAGCTAGCATT
13179926 CAAA
131 CAAA
* * *
13179930 GAAAGATTTAATTCCAAATTAGTTGGCC-TTAGAAGAAAGATTTAAGCACAAATTA
1 GAAATA-TTAATTCCAATTTAGTTGGCCTTTA-AAGAAAGATTTAAGCCCAAATTA
13179985 GCTTGCCCTC
Statistics
Matches: 161, Mismatches: 26, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
134 122 0.76
135 39 0.24
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (134 bp):
GAAATATTAATTCCAATTTAGTTGGCCTTTAAAGAAAGATTTAAGCCCAAATTAAATGGCCCTCA
AAAAAAGATTTAAGCCCAGATTAGCTAGCCACCAATGAAATATTAAGCCTAATTTAGCTAGCATT
CAAA
Found at i:13179928 original size:101 final size:102
Alignment explanation
Indices: 13179818--13180011 Score: 277
Period size: 101 Copynumber: 1.9 Consensus size: 102
13179808 CCAGTTTAGT
* * *
13179818 TGGCCTTCAAAGAAAGATTTAAGCCCAAATTAGATGGCCTTTA-AAAAAAGATTTTAGCCCAGAT
1 TGGCCTTCAAAGAAAGATTTAAGCCCAAATTAGATGGCC-TTAGAAAAAAGATTTAAGCACAAAT
13179882 TAGCTGGCCAC-CAATGAAATATTA-AGCCTAATTTTGC
65 TAGCTGGCC-CTCAATGAAATATTAGAGCCTAATTTTGC
** * *
13179919 TGGCCTTCAAAGAAAGATTTAATTCCAAATTAGTTGGCCTTAGAAGAAAGATTTAAGCACAAATT
1 TGGCCTTCAAAGAAAGATTTAAGCCCAAATTAGATGGCCTTAGAAAAAAGATTTAAGCACAAATT
*
13179984 AGCTTGCCCTCAATGAAATATTAGAGCC
66 AGCTGGCCCTCAATGAAATATTAGAGCC
13180012 AGAATAGTAG
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
100 4 0.05
101 74 0.90
102 4 0.05
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (102 bp):
TGGCCTTCAAAGAAAGATTTAAGCCCAAATTAGATGGCCTTAGAAAAAAGATTTAAGCACAAATT
AGCTGGCCCTCAATGAAATATTAGAGCCTAATTTTGC
Found at i:13179957 original size:67 final size:67
Alignment explanation
Indices: 13179718--13179940 Score: 232
Period size: 67 Copynumber: 3.3 Consensus size: 67
13179708 CCAGTTTAAA
* * * * *
13179718 TGGCCCTCAAAGAAAGATTTAAGCCCAGATTAGCTAGCTACCAATGAAATATTAAGCTTAGTTTA
1 TGGCCTTCAAAGAAAGATTTAAGCCCAGATTAGCTGGCCACCAATGAAATATTAAGCCTAATTTA
13179783 GC
66 GC
* * * * * * ** * * * *
13179785 TAGCATTCAAAGAAATA-TTAAACCCAGTTTAGTTGGCCTTCAAAGAAAGATTTAAGCCCAAATT
1 TGGCCTTCAAAGAAAGATTTAAGCCCAGATTAGCTGGCCACCAATGAAATA-TTAAGCCTAATTT
*
13179849 AGA
65 AGC
* * * *
13179852 TGGCCTTTAAAAAAAGATTTTAGCCCAGATTAGCTGGCCACCAATGAAATATTAAGCCTAATTTT
1 TGGCCTTCAAAGAAAGATTTAAGCCCAGATTAGCTGGCCACCAATGAAATATTAAGCCTAATTTA
13179917 GC
66 GC
13179919 TGGCCTTCAAAGAAAGATTTAA
1 TGGCCTTCAAAGAAAGATTTAA
13179941 TTCCAAATTA
Statistics
Matches: 116, Mismatches: 38, Indels: 4
0.73 0.24 0.03
Matches are distributed among these distances:
66 24 0.21
67 67 0.58
68 25 0.22
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.28
Consensus pattern (67 bp):
TGGCCTTCAAAGAAAGATTTAAGCCCAGATTAGCTGGCCACCAATGAAATATTAAGCCTAATTTA
GC
Found at i:13180264 original size:72 final size:72
Alignment explanation
Indices: 13180080--13181220 Score: 435
Period size: 72 Copynumber: 15.9 Consensus size: 72
13180070 CCTAGGTTAG
* * * *
13180080 CGATCATCTTGTCATTTCTCAA-TTGTGGTGTCATTCTATCATTATTCATTTCTCAACTTGCGGT
1 CGATCATCTTGTTATTTCTCAACTTGCGATGTCATTCTATCATTATTTATTTCTCAACTTGCGGT
*
13180144 GTCATTT
66 GTCATTC
* ** * *
13180151 CGATCAT-TTGTTATTTCTCAACTTGCGGTGTTGTT-TCATCATTATTCATTTCTCAACTTGCAG
1 CGATCATCTTGTTATTTCTCAACTTGCGATGTCATTCT-ATCATTATTTATTTCTCAACTTGCGG
** *
13180214 TGTGGTTT
65 TGTCATTC
* * * *
13180222 TGGTCATCTTGTTATTTATCAACTTGCGACGTCATTCTATCATTATTTATTTCTCAACTTGCGGT
1 CGATCATCTTGTTATTTCTCAACTTGCGATGTCATTCTATCATTATTTATTTCTCAACTTGCGGT
13180287 GTCATTC
66 GTCATTC
* * * * * *
13180294 CGACCATTTTGTTATTTCTCAACTTGTGATGTCATTCCATCATTATTTATTTTTCAACTTACGGT
1 CGATCATCTTGTTATTTCTCAACTTGCGATGTCATTCTATCATTATTTATTTCTCAACTTGCGGT
13180359 GTCATTC
66 GTCATTC
* * * * *
13180366 CTATCATTTTGTTATTTCTTAACTTGCGATGTCATTTTAATCATCTTTTTATTTCTCAACTTGCG
1 CGATCATCTTGTTATTTCTCAACTTGCGATGTCATTCT-ATCAT-TATTTATTTCTCAACTTGCG
13180431 GTGTCATTC
64 GTGTCATTC
* * ** * *
13180440 C-AT-A-GTTATTCATTTCTCAACTTATGATGTCATTCTGTTCATCT-TGTTATTTCTCAACTCG
1 CGATCATCTTGTT-ATTTCTCAACTTGCGATGTCATTCT-ATCAT-TAT-TTATTTCTCAACTTG
* ** * *
13180501 TGGCATCGTTT
62 CGGTGTCATTC
* * * ** * * * *
13180512 TG-T--TTTTATTTATTTCTCAACTTATGGTGTCATTCTAGTCATTTTGTTACTTCTC-ATTTGC
1 CGATCATCTT-GTTATTTCTCAACTTGCGATGTCATTCTA-TCATTAT-TTATTTCTCAACTTGC
**
13180573 AATGTCATT-
63 GGTGTCATTC
* * * * * ** **
13180582 -TATTATTATTATTCATGTT-TCAAGTTGC-AGTGTTGTTTCGGTCATCT-TGTTATTTCTCAAC
1 CGATCA-TCTTGTT-AT-TTCTCAACTTGCGA-TG-TCATTCTATCAT-TAT-TTATTTCTCAAC
** *
13180643 TTATGGTATCATTC
59 TTGCGGTGTCATTC
* * ** *
13180657 C-ATCGT-TAT-TCATTTCTCAACTTGTAATGTCGTTCTGATCATT-TTGCTATTTCTCAACTTG
1 CGATCATCT-TGTTATTTCTCAACTTGCGATGTCATTCT-ATCATTATT--TATTTCTCAACTTG
*
13180718 CGGTGTCATTT
62 CGGTGTCATTC
* * * * * ** * * * * * **
13180729 TG-TCGT-TAT-TTATTTTTTAGCTTATGATATCGTTCCATCGTTCTTTATTTCTCAACTTGTAG
1 CGATCATCT-TGTTATTTCTCAACTTGCGATGTCATTCTATCATTATTTATTTCTCAACTTGCGG
**
13180791 TGTTGTTC
65 TGTCATTC
* * * * *
13180799 TG-TCAT-TAT-TTATTTCTCAACTTACGGTGTCATTCTGGTCATTTTGTTATTTCTCAACTTGC
1 CGATCATCT-TGTTATTTCTCAACTTGCGATGTCATTCT-ATCATTAT-TTATTTCTCAACTTGC
*
13180861 GATGTCATT-
63 GGTGTCATTC
** * ** * *
13180870 TTATCAT-TAT-TCATTTCTCAACTTGCGATGTTGTTCTGATCATCT-TGTTATTTCTTAACTTA
1 CGATCATCT-TGTTATTTCTCAACTTGCGATGTCATTCT-ATCAT-TAT-TTATTTCTCAACTTG
* * ** *
13180932 CAGTATTGTTT
62 CGGTGTCATTC
* * * * * * **
13180943 CGGTCATCTTGTTATTTCTCAACTTGTGATATCATTCCATCGTTATTTATTTCTCAACTAGTAGT
1 CGATCATCTTGTTATTTCTCAACTTGCGATGTCATTCTATCATTATTTATTTCTCAACTTGCGGT
** *
13181008 GTTGTTT
66 GTCATTC
* ** * * ** * ** * *
13181015 TGGCCATTTTGTTATTTCTCAACTTAC-AGTGTTGTTTTGGCCATTTTGTTATTTCTTAACTTGC
1 CGATCATCTTGTTATTTCTCAACTTGCGA-TGTCATTCT-ATCATTAT-TTATTTCTCAACTTGC
**
13181079 AATGTCATT-
63 GGTGTCATTC
** * * * * ** * * *
13181088 TTATCAT-TAT-TCATTTCTCAATTTGCGGTGCCATTCTGCCATTATTCATTTCTCAACTTACGA
1 CGATCATCT-TGTTATTTCTCAACTTGCGATGTCATTCTATCATTATTTATTTCTCAACTTGCGG
13181151 TGTCATTC
65 TGTCATTC
* * * * * *
13181159 C-AGTCATTTTGTTATTTCTCAACTTGTGAAGTCATTCTATCGTTATTCATTTCTTAACTTGC
1 CGA-TCATCTTGTTATTTCTCAACTTGCGATGTCATTCTATCATTATTTATTTCTCAACTTGC
13181221 AATATTGTTT
Statistics
Matches: 814, Mismatches: 206, Indels: 99
0.73 0.18 0.09
Matches are distributed among these distances:
70 85 0.10
71 98 0.12
72 483 0.59
73 60 0.07
74 86 0.11
75 2 0.00
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.49
Consensus pattern (72 bp):
CGATCATCTTGTTATTTCTCAACTTGCGATGTCATTCTATCATTATTTATTTCTCAACTTGCGGT
GTCATTC
Found at i:13180318 original size:37 final size:36
Alignment explanation
Indices: 13180093--13181184 Score: 403
Period size: 35 Copynumber: 30.4 Consensus size: 36
13180083 TCATCTTGTC
* * * *
13180093 ATTTCTCAA-TTGTGGTGTCATT-CTATCATTATTC
1 ATTTCTCAACTTGCGGTGTCATTCCGATCATTTTTT
* *
13180127 ATTTCTCAACTTGCGGTGTCATTTCGATCATTTGTT
1 ATTTCTCAACTTGCGGTGTCATTCCGATCATTTTTT
** * * *
13180163 ATTTCTCAACTTGCGGTGTTGTTTC-ATCATTATTC
1 ATTTCTCAACTTGCGGTGTCATTCCGATCATTTTTT
* ** ** * *
13180198 ATTTCTCAACTTGCAGTGTGGTTTTGGTCATCTTGTT
1 ATTTCTCAACTTGCGGTGTCATTCCGATCAT-TTTTT
* ** * *
13180235 ATTTATCAACTTGCGACGTCATT-CTATCATTATTT
1 ATTTCTCAACTTGCGGTGTCATTCCGATCATTTTTT
*
13180270 ATTTCTCAACTTGCGGTGTCATTCCGACCATTTTGTT
1 ATTTCTCAACTTGCGGTGTCATTCCGATCATTTT-TT
* * *
13180307 ATTTCTCAACTTGTGATGTCATTCC-ATCATTATTT
1 ATTTCTCAACTTGCGGTGTCATTCCGATCATTTTTT
* * *
13180342 ATTTTTCAACTTACGGTGTCATTCCTATCATTTTGTT
1 ATTTCTCAACTTGCGGTGTCATTCCGATCATTTT-TT
* * ***
13180379 ATTTCTTAACTTGCGATGTCATTTTAATCATCTTTTT
1 ATTTCTCAACTTGCGGTGTCATTCCGATCAT-TTTTT
* *
13180416 ATTTCTCAACTTGCGGTGTCATTCC-AT-AGTTATTC
1 ATTTCTCAACTTGCGGTGTCATTCCGATCA-TTTTTT
** * * * *
13180451 ATTTCTCAACTTATGATGTCATTCTGTTCATCTTGTT
1 ATTTCTCAACTTGCGGTGTCATTCCGATCAT-TTTTT
* * ** * ** *
13180488 ATTTCTCAACTCGTGGCATCGTTTTG-T-TTTTATTT
1 ATTTCTCAACTTGCGGTGTCATTCCGATCATTT-TTT
** *
13180523 ATTTCTCAACTTATGGTGTCATT-CTAGTCATTTTGTT
1 ATTTCTCAACTTGCGGTGTCATTCCGA-TCATTTT-TT
* * ** * *
13180560 ACTTCTC-ATTTGCAATGTCATT--TATTATTATTATT
1 ATTTCTCAACTTGCGGTGTCATTCCGATCATT-TT-TT
* * ** * * *
13180595 CATGTT-TCAAGTTGCAGTGTTGTTTCGGTCATCTTGTT
1 -AT-TTCTCAACTTGCGGTGTCATTCCGATCAT-TTTTT
** * * * *
13180633 ATTTCTCAACTTATGGTATCATTCC-ATCGTTATTC
1 ATTTCTCAACTTGCGGTGTCATTCCGATCATTTTTT
*** * * *
13180668 ATTTCTCAACTTGTAATGTCGTTCTGATCATTTTGCT
1 ATTTCTCAACTTGCGGTGTCATTCCGATCATTTT-TT
** * *
13180705 ATTTCTCAACTTGCGGTGTCATTTTG-TCGTTATTT
1 ATTTCTCAACTTGCGGTGTCATTCCGATCATTTTTT
* * * ** * * * * *
13180740 ATTTTTTAGCTTATGATATCGTTCC-ATCGTTCTTT
1 ATTTCTCAACTTGCGGTGTCATTCCGATCATTTTTT
** ** * *
13180775 ATTTCTCAACTTGTAGTGTTGTTCTG-TCATTATTT
1 ATTTCTCAACTTGCGGTGTCATTCCGATCATTTTTT
* * *
13180810 ATTTCTCAACTTACGGTGTCATTCTGGTCATTTTGTT
1 ATTTCTCAACTTGCGGTGTCATTCCGATCATTTT-TT
* ** * *
13180847 ATTTCTCAACTTGCGATGTCATT-TTATCATTATTC
1 ATTTCTCAACTTGCGGTGTCATTCCGATCATTTTTT
* ** * *
13180882 ATTTCTCAACTTGCGATGTTGTTCTGATCATCTTGTT
1 ATTTCTCAACTTGCGGTGTCATTCCGATCAT-TTTTT
* * * * ** * * *
13180919 ATTTCTTAACTTACAGTATTGTTTCGGTCATCTTGTT
1 ATTTCTCAACTTGCGGTGTCATTCCGATCAT-TTTTT
* * * * *
13180956 ATTTCTCAACTTGTGATATCATTCC-ATCGTTATTT
1 ATTTCTCAACTTGCGGTGTCATTCCGATCATTTTTT
* ** ** ** **
13180991 ATTTCTCAACTAGTAGTGTTGTTTTGGCCATTTTGTT
1 ATTTCTCAACTTGCGGTGTCATTCCGATCATTTT-TT
* * ** ** **
13181028 ATTTCTCAACTTACAGTGTTGTTTTGGCCATTTTGTT
1 ATTTCTCAACTTGCGGTGTCATTCCGATCATTTT-TT
* ** ** * *
13181065 ATTTCTTAACTTGCAATGTCATT-TTATCATTATTC
1 ATTTCTCAACTTGCGGTGTCATTCCGATCATTTTTT
* * * * * *
13181100 ATTTCTCAATTTGCGGTGCCATTCTG-CCATTATTC
1 ATTTCTCAACTTGCGGTGTCATTCCGATCATTTTTT
* *
13181135 ATTTCTCAACTTACGATGTCATTCC-AGTCATTTTGTT
1 ATTTCTCAACTTGCGGTGTCATTCCGA-TCATTTT-TT
13181172 ATTTCTCAACTTG
1 ATTTCTCAACTTG
13181185 TGAAGTCATT
Statistics
Matches: 788, Mismatches: 230, Indels: 77
0.72 0.21 0.07
Matches are distributed among these distances:
34 15 0.02
35 317 0.40
36 134 0.17
37 312 0.40
38 5 0.01
39 4 0.01
40 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.49
Consensus pattern (36 bp):
ATTTCTCAACTTGCGGTGTCATTCCGATCATTTTTT
Found at i:13180399 original size:109 final size:108
Alignment explanation
Indices: 13180080--13181247 Score: 657
Period size: 109 Copynumber: 10.8 Consensus size: 108
13180070 CCTAGGTTAG
* * * * *
13180080 CGATCATCTTGTCATTTCTCAA-TTGTGGTGTCATTCTATCATTATTCATTTCTCAACTTGCGGT
1 CGATCATTTTGTTATTTCTCAACTTGTGATGTCATTCCATCATTATTCATTTCTCAACTTGCGAT
* * **
13180144 GTCATTTCGATCA-TTTGTTATTTCTCAACTTGCGGTGTTGTTT
66 GTCA-TTCTATCATTTTGTTATTTCTCAACTTGCGATGTCATTT
* * * * * *
13180187 C-ATCATTAT-TCATTTCTCAACTTGCAGTG-TGGT-TTTGGTCATC-TTGTT-ATTTATCAACT
1 CGATCATTTTGTTATTTCTCAACTT---GTGAT-GTCATT--CCATCATTATTCATTTCTCAACT
* * * *
13180246 TGCGACGTCATTCTATCATTAT-TTATTTCTCAACTTGCGGTGTCATTC
60 TGCGATGTCATTCTATCATTTTGTTATTTCTCAACTTGCGATGTCATTT
* * * * *
13180294 CGACCATTTTGTTATTTCTCAACTTGTGATGTCATTCCATCATTATTTATTTTTCAACTTACGGT
1 CGATCATTTTGTTATTTCTCAACTTGTGATGTCATTCCATCATTATTCATTTCTCAACTTGCGAT
*
13180359 GTCATTCCTATCATTTTGTTATTTCTTAACTTGCGATGTCATTT
66 GTCATT-CTATCATTTTGTTATTTCTCAACTTGCGATGTCATTT
** * * **
13180403 TAATCATCTTT-TTATTTCTCAACTTGCGGTGTCATTCCAT-AGTTATTCATTTCTCAACTTATG
1 CGATCAT-TTTGTTATTTCTCAACTTGTGATGTCATTCCATCA-TTATTCATTTCTCAACTTGCG
* * * * *** *
13180466 ATGTCATTCTGTTCATCTTGTTATTTCTCAACTCGTGGCATCGTTT
64 ATGTCATTCT-ATCATTTTGTTATTTCTCAACTTGCGATGTCATTT
* * * * * * * * *
13180512 TG-T--TTTTATTTATTTCTCAACTTATGGTGTCATTCTAGTCATTTTGTTACTTCTC-ATTTGC
1 CGATCATTTT-GTTATTTCTCAACTTGTGATGTCATTCCA-TCATTAT-TCATTTCTCAACTTGC
* * * * **
13180573 AATGTCATT-TATTATTATTATTCATGTT-TCAAGTTGC-AGTGTTGTTT
63 GATGTCATTCTATCATT-TTGTT-AT-TTCTCAACTTGCGA-TGTCATTT
* * * * * * **
13180620 CGGTCATCTTGTTATTTCTCAACTTATGGTATCATTCCATCGTTATTCATTTCTCAACTTGTAAT
1 CGATCATTTTGTTATTTCTCAACTTGTGATGTCATTCCATCATTATTCATTTCTCAACTTGCGAT
* * *
13180685 GTCGTTCTGATCATTTTGCTATTTCTCAACTTGCGGTGTCATTT
66 GTCATTCT-ATCATTTTGTTATTTCTCAACTTGCGATGTCATTT
* * * * * * * * * * * * *
13180729 TG-TCGTTAT-TTATTTTTTAGCTTATGATATCGTTCCATCGTTCTTTATTTCTCAACTTG-TAG
1 CGATCATTTTGTTATTTCTCAACTTGTGATGTCATTCCATCATTATTCATTTCTCAACTTGCGA-
** * * * *
13180791 TGTTGTTCTGTCATTAT-TTATTTCTCAACTTACGGTGTCA-TT
65 TGTCATTCTATCATTTTGTTATTTCTCAACTTGCGATGTCATTT
* * **
13180833 CTGGTCATTTTGTTATTTCTCAACTTGCGATGTCATTTTATCATTATTCATTTCTCAACTTGCGA
1 C-GATCATTTTGTTATTTCTCAACTTGTGATGTCATTCCATCATTATTCATTTCTCAACTTGCGA
** * * * *
13180898 TGTTGTTCTGATCATCTTGTTATTTCTTAACTTACAGTAT-T-GTTT
65 TGTCATTCT-ATCATTTTGTTATTTCTCAACTTGC-G-ATGTCATTT
* * * * * * *
13180943 CGGTCATCTTGTTATTTCTCAACTTGTGATATCATTCCATCGTTATTTATTTCTCAACTAG-TAG
1 CGATCATTTTGTTATTTCTCAACTTGTGATGTCATTCCATCATTATTCATTTCTCAACTTGCGA-
** * ** * **
13181007 TGTTGTTTTGGCCATTTTGTTATTTCTCAACTTAC-AGTGTTGTTT
65 TGTCATTCT-ATCATTTTGTTATTTCTCAACTTGCGA-TGTCATTT
* ** * ** ** * *
13181052 TGGCCATTTTGTTATTTCTTAACTTGCAATGTCATTTTATCATTATTCATTTCTCAATTTGCGGT
1 CGATCATTTTGTTATTTCTCAACTTGTGATGTCATTCCATCATTATTCATTTCTCAACTTGCGAT
* ** * * *
13181117 GCCATTCTGCCATTAT-TCATTTCTCAACTTACGATGTCA-TT
66 GTCATTCTATCATTTTGTTATTTCTCAACTTGCGATGTCATTT
* * * * * *
13181158 CCAGTCATTTTGTTATTTCTCAACTTGTGAAGTCATTCTATCGTTATTCATTTCTTAACTTGCAA
1 CGA-TCATTTTGTTATTTCTCAACTTGTGATGTCATTCCATCATTATTCATTTCTCAACTTGCGA
* ** *
13181223 TATTGTTTCGATCATTTTGTTATTT
65 T-GTCATTCTATCATTTTGTTATTT
13181248 TTTGACTTAT
Statistics
Matches: 820, Mismatches: 186, Indels: 108
0.74 0.17 0.10
Matches are distributed among these distances:
104 2 0.00
105 40 0.05
106 36 0.04
107 252 0.31
108 108 0.13
109 332 0.40
110 41 0.05
111 9 0.01
ACGTcount: A:0.19, C:0.18, G:0.13, T:0.49
Consensus pattern (108 bp):
CGATCATTTTGTTATTTCTCAACTTGTGATGTCATTCCATCATTATTCATTTCTCAACTTGCGAT
GTCATTCTATCATTTTGTTATTTCTCAACTTGCGATGTCATTT
Found at i:13183261 original size:30 final size:32
Alignment explanation
Indices: 13183225--13183305 Score: 103
Period size: 32 Copynumber: 2.6 Consensus size: 32
13183215 TGCTATTGCA
*
13183225 GTTTGGTTTGCCTACAT-T-TTTGTTGTTTCG
1 GTTTGGTTTGCCTACATATGTTGGTTGTTTCG
*
13183255 GTTTGGTTTACCTACATATGTTGGTTGTTTCG
1 GTTTGGTTTGCCTACATATGTTGGTTGTTTCG
* * *
13183287 GGTTGGTATGCCTGCATAT
1 GTTTGGTTTGCCTACATAT
13183306 ATTTGCTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 16 0.37
31 1 0.02
32 26 0.60
ACGTcount: A:0.11, C:0.14, G:0.26, T:0.49
Consensus pattern (32 bp):
GTTTGGTTTGCCTACATATGTTGGTTGTTTCG
Found at i:13183349 original size:32 final size:32
Alignment explanation
Indices: 13183313--13183384 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
13183303 TATATTTGCT
*
13183313 ATTTGGTTTACCTACATGTGTTAACTATTTCA
1 ATTTGGTTTACCTACATCTGTTAACTATTTCA
* * ** *
13183345 ATTTGGGTTGCCTGTATCTGTTTACTATTTCA
1 ATTTGGTTTACCTACATCTGTTAACTATTTCA
*
13183377 ATTGGGTT
1 ATTTGGTT
13183385 AACTTGCATA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.49
Consensus pattern (32 bp):
ATTTGGTTTACCTACATCTGTTAACTATTTCA
Found at i:13184019 original size:3 final size:3
Alignment explanation
Indices: 13184011--13184059 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
13184001 CTACAAAGAC
13184011 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
13184058 AT
1 AT
13184060 TTTAAAGCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:13198487 original size:18 final size:18
Alignment explanation
Indices: 13198459--13198502 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
13198449 TTATGGATTG
13198459 TGATATTGGTATA-TGCT
1 TGATATTGGTATATTGCT
13198476 TGATAGTTGGTATATTGCT
1 TGATA-TTGGTATATTGCT
13198495 TGATATTG
1 TGATATTG
13198503 AGATTGGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.20
18 11 0.44
19 9 0.36
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.48
Consensus pattern (18 bp):
TGATATTGGTATATTGCT
Found at i:13198694 original size:72 final size:71
Alignment explanation
Indices: 13198609--13198751 Score: 232
Period size: 72 Copynumber: 2.0 Consensus size: 71
13198599 AAAAGGGGAG
* * *
13198609 AGGCAATGGTATGAAAATTTTCTATTTGATTGATGATCTTGATGGTATGAATAAATTCTCACTTG
1 AGGCAATGGTATGAAAATTTTCTATTTAATTGATGATCTTGAT-GTATGAACAAATTCCCACTTG
13198674 ATGATAT
65 ATGATAT
* *
13198681 AGGCAGTGGTATGAAAATTTTCTATTTAATTGATGATCTTGATGTATGAACAAATTCCCGCTTGA
1 AGGCAATGGTATGAAAATTTTCTATTTAATTGATGATCTTGATGTATGAACAAATTCCCACTTGA
13198746 TGATAT
66 TGATAT
13198752 TGACATTGTT
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
71 25 0.38
72 41 0.62
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (71 bp):
AGGCAATGGTATGAAAATTTTCTATTTAATTGATGATCTTGATGTATGAACAAATTCCCACTTGA
TGATAT
Found at i:13200589 original size:29 final size:30
Alignment explanation
Indices: 13200557--13200617 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
13200547 TTCAAACCCC
13200557 TTTT-TTTTTATTTT-TTCTTCATTTTTTTA
1 TTTTGTTTTTATTTTATTCTT-ATTTTTTTA
* *
13200586 TTTTGTTTTTGTTTTGATTCTTTTTTTTTTA
1 TTTTGTTTTTATTTT-ATTCTTATTTTTTTA
13200617 T
1 T
13200618 AAAGAATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 4 0.15
30 9 0.33
31 9 0.33
32 5 0.19
ACGTcount: A:0.08, C:0.05, G:0.05, T:0.82
Consensus pattern (30 bp):
TTTTGTTTTTATTTTATTCTTATTTTTTTA
Found at i:13201276 original size:17 final size:16
Alignment explanation
Indices: 13201247--13201286 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
13201237 CAAAATATTT
13201247 TTTTTTATTTTTTC-C
1 TTTTTTATTTTTTCTC
13201262 ATTTTTTATTTTTTTCTC
1 -TTTTTTA-TTTTTTCTC
13201280 TTTTTTA
1 TTTTTTA
13201287 AAAAACAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.32
17 14 0.64
18 1 0.05
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTATTTTTTCTC
Found at i:13202370 original size:13 final size:14
Alignment explanation
Indices: 13202352--13202380 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
13202342 AAGGTTTGGG
13202352 TTTAGGTTTA-AGT
1 TTTAGGTTTAGAGT
13202365 TTTAGGTTTAGAGT
1 TTTAGGTTTAGAGT
13202379 TT
1 TT
13202381 AGAGTATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.21, C:0.00, G:0.24, T:0.55
Consensus pattern (14 bp):
TTTAGGTTTAGAGT
Found at i:13208729 original size:84 final size:84
Alignment explanation
Indices: 13208577--13208732 Score: 240
Period size: 84 Copynumber: 1.9 Consensus size: 84
13208567 ATTCTTTTAG
* **
13208577 GCAAGATTCATAAGTCATCTAAGCAAAATTTGTTTTAGTGTCAAGATTTATAAAACCTCCTAGCA
1 GCAAGATTCATAAGTCATCTAAGCAAAATCTGTTTTAGTGTCAAGATTTATAAAACCTCAAAGCA
13208642 TAGTCTCTAGAACCTCCAA
66 TAGTCTCTAGAACCTCCAA
* ** * *
13208661 GCAAGATTTATAAGTTTTCTAAGCAAAATCTGTTTTAGTGTCAAGATTTATAAAATCTCAAAGGA
1 GCAAGATTCATAAGTCATCTAAGCAAAATCTGTTTTAGTGTCAAGATTTATAAAACCTCAAAGCA
13208726 TAGTCTC
66 TAGTCTC
13208733 ATGACCTTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
84 64 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (84 bp):
GCAAGATTCATAAGTCATCTAAGCAAAATCTGTTTTAGTGTCAAGATTTATAAAACCTCAAAGCA
TAGTCTCTAGAACCTCCAA
Found at i:13220191 original size:24 final size:22
Alignment explanation
Indices: 13220147--13220192 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
13220137 ATAATGTTTA
*
13220147 ATGAAAATTTATCATCTAATTC
1 ATGAAAATGTATCATCTAATTC
*
13220169 ATGAATAATGTATACATTTAATTC
1 ATGAA-AATGTAT-CATCTAATTC
13220193 TCATAATCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 6 0.30
24 9 0.45
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (22 bp):
ATGAAAATGTATCATCTAATTC
Found at i:13220428 original size:100 final size:100
Alignment explanation
Indices: 13220255--13220448 Score: 262
Period size: 100 Copynumber: 1.9 Consensus size: 100
13220245 TTTTTACAAG
* * *
13220255 TAAATTCTAAGCTTATATCTTCTAATTTTATTACATAAAATACAATAGACTTTTAATTGTCTAAT
1 TAAATTCTAAGCTTATATCTCCTAATTATATTACATAAAACACAATAGACTTTTAATTGTCTAAT
* * *
13220320 ATTTATATGTATTTTTTACTTTTGATTTTCTTCTA
66 ATTTATATGTATTCTTGACATTTGATTTTCTTCTA
* * * * * ** *
13220355 TAAATTTTAAGCTTATATCTCCTAATTATATTATATAAAACATAATGGATTTTTGGTTGTTTAAT
1 TAAATTCTAAGCTTATATCTCCTAATTATATTACATAAAACACAATAGACTTTTAATTGTCTAAT
13220420 ATTTATATGTATTCTTGACATTTGATTTT
66 ATTTATATGTATTCTTGACATTTGATTTT
13220449 TTTTCTATTC
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
100 80 1.00
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.52
Consensus pattern (100 bp):
TAAATTCTAAGCTTATATCTCCTAATTATATTACATAAAACACAATAGACTTTTAATTGTCTAAT
ATTTATATGTATTCTTGACATTTGATTTTCTTCTA
Found at i:13224269 original size:36 final size:35
Alignment explanation
Indices: 13224184--13224372 Score: 113
Period size: 36 Copynumber: 5.4 Consensus size: 35
13224174 TAAAGTTCAT
* *
13224184 ACATATATAATAAATATTTTATTCTTTCTTTTCAC
1 ACATATATAATAAATATTTTATTCTTTCTTCTCAA
* * * * *
13224219 ACATATACAGTAAATTTTTTGTTTTTTTCTTCTCAA
1 ACATATATAATAAATATTTT-ATTCTTTCTTCTCAA
* ** **
13224255 ACATATATAATAAATCTTTGGTTC-AGCATATACTTC-A
1 ACATATATAATAAATATTTTATTCTTTC-T-T-C-TCAA
* *
13224292 AC--ATATAAT---TATTTTATTCTTTCTTTTCAC
1 ACATATATAATAAATATTTTATTCTTTCTTCTCAA
* * * *
13224322 ACATATACAGTAAATATTTTGTTTTTTTCTTCTCAA
1 ACATATATAATAAATATTTT-ATTCTTTCTTCTCAA
13224358 ACATATATAATAAAT
1 ACATATATAATAAAT
13224373 CTTTGGTTCA
Statistics
Matches: 111, Mismatches: 30, Indels: 25
0.67 0.18 0.15
Matches are distributed among these distances:
29 2 0.02
30 2 0.02
31 1 0.01
32 13 0.12
33 1 0.01
34 1 0.01
35 33 0.30
36 52 0.47
37 4 0.04
38 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.04, T:0.48
Consensus pattern (35 bp):
ACATATATAATAAATATTTTATTCTTTCTTCTCAA
Found at i:13224314 original size:103 final size:103
Alignment explanation
Indices: 13224193--13224409 Score: 416
Period size: 103 Copynumber: 2.1 Consensus size: 103
13224183 TACATATATA
* *
13224193 ATAAATATTTTATTCTTTCTTTTCACACATATACAGTAAATTTTTTGTTTTTTTCTTCTCAAACA
1 ATAATTATTTTATTCTTTCTTTTCACACATATACAGTAAATATTTTGTTTTTTTCTTCTCAAACA
13224258 TATATAATAAATCTTTGGTTCAGCATATACTTCAACAT
66 TATATAATAAATCTTTGGTTCAGCATATACTTCAACAT
13224296 ATAATTATTTTATTCTTTCTTTTCACACATATACAGTAAATATTTTGTTTTTTTCTTCTCAAACA
1 ATAATTATTTTATTCTTTCTTTTCACACATATACAGTAAATATTTTGTTTTTTTCTTCTCAAACA
13224361 TATATAATAAATCTTTGGTTCAGCATATACTTCAACAT
66 TATATAATAAATCTTTGGTTCAGCATATACTTCAACAT
13224399 ATAATTATTTT
1 ATAATTATTTT
13224410 TTTTCCAAAA
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.32, C:0.15, G:0.05, T:0.48
Consensus pattern (103 bp):
ATAATTATTTTATTCTTTCTTTTCACACATATACAGTAAATATTTTGTTTTTTTCTTCTCAAACA
TATATAATAAATCTTTGGTTCAGCATATACTTCAACAT
Found at i:13225016 original size:28 final size:28
Alignment explanation
Indices: 13224955--13225016 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 28
13224945 TTTTGTATAA
*
13224955 ATATAATATTTTATTAAATTAAGATATT
1 ATATAATATTTTATTAAATTAAGACATT
* *
13224983 AAATAATAATTTTATT-AATATAATACA-T
1 ATATAAT-ATTTTATTAAAT-TAAGACATT
13225011 ATATAA
1 ATATAA
13225017 CTAAAATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (28 bp):
ATATAATATTTTATTAAATTAAGACATT
Found at i:13235881 original size:20 final size:20
Alignment explanation
Indices: 13235856--13235900 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
13235846 TTAAATAAAC
* *
13235856 AAATAAATAATTTATATTTT
1 AAATAAATAATTTACATGTT
13235876 AAATAAATAATTTACATGTT
1 AAATAAATAATTTACATGTT
13235896 AAATA
1 AAATA
13235901 TATTATATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
AAATAAATAATTTACATGTT
Found at i:13237478 original size:25 final size:25
Alignment explanation
Indices: 13237439--13237527 Score: 69
Period size: 25 Copynumber: 3.6 Consensus size: 25
13237429 AAAAAAATAA
* *
13237439 AAAACAATTATAATAAGAAACAAGC
1 AAAACATTTAAAATAAGAAACAAGC
*
13237464 AAAACATTTAAAATAA-ATAATAAAG-
1 AAAACATTTAAAATAAGA-AA-CAAGC
* * *
13237489 ATAACA--AAATAATAAGAAACAAAC
1 AAAACATTTAA-AATAAGAAACAAGC
13237513 AAAACATTTAAAATA
1 AAAACATTTAAAATA
13237528 GATAATAAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 14
0.68 0.13 0.20
Matches are distributed among these distances:
23 4 0.08
24 13 0.27
25 26 0.54
26 5 0.10
ACGTcount: A:0.67, C:0.09, G:0.04, T:0.19
Consensus pattern (25 bp):
AAAACATTTAAAATAAGAAACAAGC
Found at i:13237500 original size:17 final size:15
Alignment explanation
Indices: 13237478--13237511 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
13237468 CATTTAAAAT
13237478 AAATAATAAAGATAACA
1 AAATAAT-AAGA-AACA
13237495 AAATAATAAGAAACA
1 AAATAATAAGAAACA
13237510 AA
1 AA
13237512 CAAAACATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 4 0.24
17 7 0.41
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.15
Consensus pattern (15 bp):
AAATAATAAGAAACA
Found at i:13237503 original size:49 final size:49
Alignment explanation
Indices: 13237437--13237546 Score: 166
Period size: 49 Copynumber: 2.2 Consensus size: 49
13237427 GCAAAAAAAT
* *
13237437 AAAAAACAATTATAATAAGAAACAAGCAAAACATTTAAAATAAATAATAA
1 AAAAAACAA-AATAATAAGAAACAAACAAAACATTTAAAATAAATAATAA
* * *
13237487 AGATAACAAAATAATAAGAAACAAACAAAACATTTAAAATAGATAATAA
1 AAAAAACAAAATAATAAGAAACAAACAAAACATTTAAAATAAATAATAA
13237536 AAAAAACAAAA
1 AAAAAACAAAA
13237547 AGAAAAGAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
49 46 0.87
50 7 0.13
ACGTcount: A:0.70, C:0.08, G:0.05, T:0.17
Consensus pattern (49 bp):
AAAAAACAAAATAATAAGAAACAAACAAAACATTTAAAATAAATAATAA
Found at i:13243030 original size:30 final size:30
Alignment explanation
Indices: 13242991--13243051 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
13242981 GAGAAATTGC
13242991 TGATCTTTGATTAATGTGAATAATTATCTA
1 TGATCTTTGATTAATGTGAATAATTATCTA
*
13243021 TGATTTTTGATTAATGTGAATAATTATCTA
1 TGATCTTTGATTAATGTGAATAATTATCTA
13243051 T
1 T
13243052 TTATATATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (30 bp):
TGATCTTTGATTAATGTGAATAATTATCTA
Found at i:13243082 original size:13 final size:13
Alignment explanation
Indices: 13243056--13243089 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
13243046 ATCTATTTAT
*
13243056 ATATAATATGTTA
1 ATATAATATATTA
*
13243069 ATATATTATATTA
1 ATATAATATATTA
13243082 ATATAATA
1 ATATAATA
13243090 AATATATCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
ATATAATATATTA
Found at i:13243460 original size:41 final size:42
Alignment explanation
Indices: 13243391--13243472 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 42
13243381 TGGTTTTAAT
* * **
13243391 TGATGAAGGTTGAGAATAACAGGGAATAAGAA-GAACAAAGA
1 TGATAAAGGATGAGAATAACAGAAAATAAGAATGAACAAAGA
* *
13243432 TGATAAAGGATGAGAATAAGAGAAAATAAGAATGAATAAAG
1 TGATAAAGGATGAGAATAACAGAAAATAAGAATGAACAAAG
13243473 GGAAAATAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 27 0.79
42 7 0.21
ACGTcount: A:0.55, C:0.02, G:0.27, T:0.16
Consensus pattern (42 bp):
TGATAAAGGATGAGAATAACAGAAAATAAGAATGAACAAAGA
Found at i:13247016 original size:11 final size:11
Alignment explanation
Indices: 13247000--13247028 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
13246990 TTCTAGATAG
13247000 AAAGAGAGAAA
1 AAAGAGAGAAA
13247011 AAAGAGAGAAA
1 AAAGAGAGAAA
13247022 AAAGAGA
1 AAAGAGA
13247029 AAGGAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (11 bp):
AAAGAGAGAAA
Found at i:13247309 original size:13 final size:13
Alignment explanation
Indices: 13247293--13247334 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
13247283 TTTGTTTTGG
13247293 TATTT-TTTAATTT
1 TATTTATTT-ATTT
13247306 TATTTATTTATTT
1 TATTTATTTATTT
*
13247319 TATTTAATTAGTTT
1 TATTTATTTA-TTT
13247333 TA
1 TA
13247335 CATGATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 18 0.69
14 8 0.31
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (13 bp):
TATTTATTTATTT
Found at i:13248050 original size:49 final size:48
Alignment explanation
Indices: 13247967--13248063 Score: 133
Period size: 49 Copynumber: 2.0 Consensus size: 48
13247957 GTTTTTTTTT
*
13247967 TTTTAAATAGACCTAAATGGTGAAATTTCAAAAATAAAACTTGTAAAAA
1 TTTTAAATAGACCTAAATGGTAAAATTT-AAAAATAAAACTTGTAAAAA
* *
13248016 TTTTAAATTGACTTAAATGGTAAAAAATTT-AAAATAAAACTTGTAAAA
1 TTTTAAATAGACCTAAATGGT--AAAATTTAAAAATAAAACTTGTAAAA
13248064 TAAAAAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
49 37 0.86
51 6 0.14
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (48 bp):
TTTTAAATAGACCTAAATGGTAAAATTTAAAAATAAAACTTGTAAAAA
Found at i:13257865 original size:43 final size:43
Alignment explanation
Indices: 13257818--13257950 Score: 162
Period size: 43 Copynumber: 3.1 Consensus size: 43
13257808 AAGCCTTTGT
* *
13257818 TTAGAATAGGTTTATTTATTTTTTAAAGTTATTGAGTGTCTAC
1 TTAGAATAGTTTTATTTATTTTTTAAAGTTATTGAGTCTCTAC
* * *
13257861 TTAGAGA-AGTTTTATTTATTTTTTAAAATTGTTGAGTCTTTAC
1 TTAGA-ATAGTTTTATTTATTTTTTAAAGTTATTGAGTCTCTAC
* * * *
13257904 TTAG-ATATTTTTTTTTATTTTTTCAAGTTATTGAGCCTCTAC
1 TTAGAATAGTTTTATTTATTTTTTAAAGTTATTGAGTCTCTAC
13257946 TTAGA
1 TTAGA
13257951 GGAATTTTAC
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
41 1 0.01
42 33 0.44
43 40 0.53
44 1 0.01
ACGTcount: A:0.26, C:0.07, G:0.14, T:0.53
Consensus pattern (43 bp):
TTAGAATAGTTTTATTTATTTTTTAAAGTTATTGAGTCTCTAC
Found at i:13262609 original size:89 final size:89
Alignment explanation
Indices: 13262458--13262633 Score: 307
Period size: 89 Copynumber: 2.0 Consensus size: 89
13262448 GAAAGGGTTT
* *
13262458 AAATAAATAATTTTTACCTCCAACTAAGAATACATGATGAATTGCAATTATAGTAAAATTTTTCT
1 AAATAAATAATTTTTACCTCCAACAAAGAATACATGATGAATCGCAATTATAGTAAAATTTTTCT
13262523 TAATTAATATTGGACTTATTCATC
66 TAATTAATATTGGACTTATTCATC
* *
13262547 AAATAAATAATTTTTACCTCCAACAAAGAATACATGATGAATCGCAATTATGGTAAAGTTTTTCT
1 AAATAAATAATTTTTACCTCCAACAAAGAATACATGATGAATCGCAATTATAGTAAAATTTTTCT
*
13262612 TAATTAATATTTGACTTATTCA
66 TAATTAATATTGGACTTATTCA
13262634 ACAAGTAATC
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
89 82 1.00
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (89 bp):
AAATAAATAATTTTTACCTCCAACAAAGAATACATGATGAATCGCAATTATAGTAAAATTTTTCT
TAATTAATATTGGACTTATTCATC
Found at i:13262912 original size:28 final size:29
Alignment explanation
Indices: 13262881--13262951 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
13262871 TAATACATTA
13262881 ATTAATAAA-TTTATAA-TTTAAATATCAT
1 ATTAA-AAATTTTATAAGTTTAAATATCAT
* * *
13262909 ATTAAAAATTTTTTAAGTTTAAGTCTCAT
1 ATTAAAAATTTTATAAGTTTAAATATCAT
*
13262938 ATTAAATATTTTAT
1 ATTAAAAATTTTAT
13262952 TTTAATTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 3 0.08
28 11 0.31
29 22 0.61
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (29 bp):
ATTAAAAATTTTATAAGTTTAAATATCAT
Found at i:13267581 original size:17 final size:17
Alignment explanation
Indices: 13267556--13267600 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
13267546 AAAATACAAC
*
13267556 AAAAACAAAAGAAA-AA
1 AAAAACAAAACAAATAA
13267572 AAAAAGCAAAACAAATAA
1 AAAAA-CAAAACAAATAA
13267590 AAAATACAAAA
1 AAAA-ACAAAA
13267601 AAAGGAGAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 5 0.20
17 8 0.32
18 11 0.44
19 1 0.04
ACGTcount: A:0.82, C:0.09, G:0.04, T:0.04
Consensus pattern (17 bp):
AAAAACAAAACAAATAA
Found at i:13269217 original size:30 final size:30
Alignment explanation
Indices: 13269183--13269362 Score: 79
Period size: 28 Copynumber: 6.2 Consensus size: 30
13269173 GATAATAATA
*
13269183 AAAACCAAAAAACCCTCCGAA-CCTAAAATC
1 AAAACC-AAAAACCCTCCAAACCCTAAAATC
** *
13269213 AAAACCCTAAATCCTCCAAACCCTAAAATC
1 AAAACCAAAAACCCTCCAAACCCTAAAATC
*** * * * *
13269243 AAAACTTCAAA-CCT-AAAATCTTAAGATC
1 AAAACCAAAAACCCTCCAAACCCTAAAATC
* ** *
13269271 GAAACCCCAAA-CCT-CAAACCCTAATATC
1 AAAACCAAAAACCCTCCAAACCCTAAAATC
* * ***
13269299 GAAACCATAAATTTTCCAAACCCTAAAA-C
1 AAAACCAAAAACCCTCCAAACCCTAAAATC
** *
13269328 TAAAACCCTAAA--CTCCAAACCTTAAAATC
1 -AAAACCAAAAACCCTCCAAACCCTAAAATC
13269357 AAAACC
1 AAAACC
13269363 CTAAACATTG
Statistics
Matches: 118, Mismatches: 27, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
28 59 0.50
29 16 0.14
30 43 0.36
ACGTcount: A:0.49, C:0.32, G:0.02, T:0.17
Consensus pattern (30 bp):
AAAACCAAAAACCCTCCAAACCCTAAAATC
Found at i:13269223 original size:14 final size:14
Alignment explanation
Indices: 13269204--13269367 Score: 73
Period size: 14 Copynumber: 11.4 Consensus size: 14
13269194 ACCCTCCGAA
13269204 CCTAAAATCAAAAC
1 CCTAAAATCAAAAC
* *
13269218 CCTAAATCCTCCAAAC
1 CCTAAA--ATCAAAAC
13269234 CCTAAAATCAAAA-
1 CCTAAAATCAAAAC
* * * *
13269247 CTTCAAACCTAAAAT
1 CCTAAAATC-AAAAC
* * *
13269262 CTTAAGATCGAAAC
1 CCTAAAATCAAAAC
* *
13269276 CCCAAACCTC-AAAC
1 CCTAAA-ATCAAAAC
* *
13269290 CCTAATATCGAAAC
1 CCTAAAATCAAAAC
* * *
13269304 CATAAATTTTCCAAAC
1 CCTAAA--ATCAAAAC
13269320 CCTAAAA-CTAAAAC
1 CCTAAAATC-AAAAC
* *
13269334 CCTAAACTCCAAAC
1 CCTAAAATCAAAAC
*
13269348 CTTAAAATCAAAAC
1 CCTAAAATCAAAAC
13269362 CCTAAA
1 CCTAAA
13269368 CATTGAAACT
Statistics
Matches: 108, Mismatches: 32, Indels: 20
0.68 0.20 0.12
Matches are distributed among these distances:
13 9 0.08
14 67 0.62
15 9 0.08
16 23 0.21
ACGTcount: A:0.48, C:0.31, G:0.02, T:0.19
Consensus pattern (14 bp):
CCTAAAATCAAAAC
Found at i:13269353 original size:28 final size:28
Alignment explanation
Indices: 13269204--13269368 Score: 122
Period size: 28 Copynumber: 5.8 Consensus size: 28
13269194 ACCCTCCGAA
13269204 CCTAAAATCAAAACCCTAAATCCTCCAAAC
1 CCTAAAATCAAAACCCTAAA--CTCCAAAC
* * *
13269234 CCTAAAATCAAAA-CTTCAAAC-CTAAAAT
1 CCTAAAATCAAAACCCT-AAACTC-CAAAC
* * * *
13269262 CTTAAGATCGAAACCCCAAAC-CTCAAAC
1 CCTAAAATCAAAACCCTAAACTC-CAAAC
* * * *
13269290 CCTAATATCGAAACCATAAATTTTCCAAAC
1 CCTAAAATCAAAACCCTAAA--CTCCAAAC
13269320 CCTAAAA-CTAAAACCCTAAACTCCAAAC
1 CCTAAAATC-AAAACCCTAAACTCCAAAC
*
13269348 CTTAAAATCAAAACCCTAAAC
1 CCTAAAATCAAAACCCTAAAC
13269369 ATTGAAACTC
Statistics
Matches: 107, Mismatches: 20, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
27 1 0.01
28 64 0.60
29 5 0.05
30 36 0.34
31 1 0.01
ACGTcount: A:0.48, C:0.32, G:0.02, T:0.19
Consensus pattern (28 bp):
CCTAAAATCAAAACCCTAAACTCCAAAC
Found at i:13269525 original size:15 final size:15
Alignment explanation
Indices: 13269505--13269546 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
13269495 ACCTTAAAAT
13269505 CTAAAATCTCAAACC
1 CTAAAATCTCAAACC
* *
13269520 CTAAAATTTGAAACC
1 CTAAAATCTCAAACC
*
13269535 TTAAAATC-CAAA
1 CTAAAATCTCAAA
13269547 AATCTAAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
14 3 0.14
15 19 0.86
ACGTcount: A:0.50, C:0.24, G:0.02, T:0.24
Consensus pattern (15 bp):
CTAAAATCTCAAACC
Found at i:13271023 original size:19 final size:19
Alignment explanation
Indices: 13270999--13271037 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
13270989 AATGAAATGT
*
13270999 GTAAATCCATTGTCCTAAA
1 GTAAATCCATTGTCCCAAA
*
13271018 GTAAATCTATTGTCCCAAA
1 GTAAATCCATTGTCCCAAA
13271037 G
1 G
13271038 AACCGCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.31
Consensus pattern (19 bp):
GTAAATCCATTGTCCCAAA
Found at i:13271448 original size:14 final size:15
Alignment explanation
Indices: 13271406--13271448 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
13271396 TTTTTATTTA
*
13271406 TATATATTTATATAAT
1 TATATATTTA-AAAAT
13271422 TATATATTT-AAAAT
1 TATATATTTAAAAAT
13271436 T-TATATTTAAAAA
1 TATATATTTAAAAA
13271449 AATAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 7 0.28
14 9 0.36
16 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATATATTTAAAAAT
Found at i:13271471 original size:21 final size:22
Alignment explanation
Indices: 13271435--13271482 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
13271425 ATATTTAAAA
*
13271435 TTTATATTTAAAAAAATAATTT
1 TTTATATTTAAAAAAATAATAT
13271457 TTTATATTT-AAAAAATAATAT
1 TTTATATTTAAAAAAATAATAT
13271478 TTTAT
1 TTTAT
13271483 TAATTTCGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTATATTTAAAAAAATAATAT
Found at i:13271978 original size:30 final size:30
Alignment explanation
Indices: 13271937--13271993 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
13271927 TTAATTATTT
* * *
13271937 ATATATATATTTATATAATGATATTTTTAA
1 ATATATATATTTAAAAAATAATATTTTTAA
*
13271967 ATATTTATATTTAAAAAATAATATTTT
1 ATATATATATTTAAAAAATAATATTTT
13271994 ATATTTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
ATATATATATTTAAAAAATAATATTTTTAA
Found at i:13271996 original size:21 final size:22
Alignment explanation
Indices: 13271966--13272017 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
13271956 GATATTTTTA
13271966 AATA-TTTATA-TTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
13271986 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
13272008 AATATTTTAT
1 AATATTTTAT
13272018 TAATTTCGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 20 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:13272834 original size:30 final size:30
Alignment explanation
Indices: 13272774--13272868 Score: 117
Period size: 30 Copynumber: 3.2 Consensus size: 30
13272764 TTAATGCGTT
*
13272774 ATAAA-TATATAA-ATTTTATTTATT-ATTA
1 ATAAATTATATAATATTAT-TTTATTAATTA
*
13272802 ATAAATTGA-ATGATATTATTTTATTAATTA
1 ATAAATT-ATATAATATTATTTTATTAATTA
*
13272832 ATAAATTATATAATATTATTTTATTAATAA
1 ATAAATTATATAATATTATTTTATTAATTA
13272862 ATAAATT
1 ATAAATT
13272869 TTAAAAATAT
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
28 5 0.09
29 11 0.19
30 42 0.72
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (30 bp):
ATAAATTATATAATATTATTTTATTAATTA
Found at i:13272879 original size:36 final size:34
Alignment explanation
Indices: 13272839--13272920 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 34
13272829 TTAATAAATT
13272839 ATATAATATTATTTTATTAATAAATAAATTTTAAAA
1 ATATAATATTATTTT-TT-ATAAATAAATTTTAAAA
* **
13272875 ATATATATATTAATTTTTTATATATTTATTTTAAAA
1 ATATA-ATATT-ATTTTTTATAAATAAATTTTAAAA
13272911 AT-TAATATTA
1 ATATAATATTA
13272921 AATTACTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
33 1 0.02
34 5 0.12
35 2 0.05
36 21 0.51
37 7 0.17
38 5 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (34 bp):
ATATAATATTATTTTTTATAAATAAATTTTAAAA
Found at i:13273195 original size:2 final size:2
Alignment explanation
Indices: 13273188--13273213 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13273178 GAGTCCAAGA
13273188 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
13273214 TCACTCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13273721 original size:19 final size:18
Alignment explanation
Indices: 13273697--13273734 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
13273687 ACTTGAATGC
13273697 AATGAGTTTGAGTTCTGAA
1 AATGAGTTTGAGTT-TGAA
13273716 AATGAGTTTGAGTTTGAA
1 AATGAGTTTGAGTTTGAA
13273734 A
1 A
13273735 TTTAATTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (18 bp):
AATGAGTTTGAGTTTGAA
Found at i:13277542 original size:3 final size:3
Alignment explanation
Indices: 13277536--13277576 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
13277526 AAATTAAATA
13277536 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
13277577 ATGGTGTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:13278982 original size:21 final size:22
Alignment explanation
Indices: 13278939--13278981 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
13278929 AAACAACATG
13278939 AAAAAAATCATATATATGTTTT
1 AAAAAAATCATATATATGTTTT
*
13278961 AAAAAAA-CATATTTCATGTTT
1 AAAAAAATCATATAT-ATGTTT
13278982 ATTCATATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.40
Consensus pattern (22 bp):
AAAAAAATCATATATATGTTTT
Found at i:13279763 original size:14 final size:14
Alignment explanation
Indices: 13279744--13279770 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13279734 TAAGGATGTT
13279744 TGTATATACAAATA
1 TGTATATACAAATA
13279758 TGTATATACAAAT
1 TGTATATACAAAT
13279771 GCCACTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (14 bp):
TGTATATACAAATA
Found at i:13279881 original size:34 final size:34
Alignment explanation
Indices: 13279843--13279926 Score: 87
Period size: 34 Copynumber: 2.5 Consensus size: 34
13279833 AACTGTCACT
** *
13279843 AATTTAGTGACATTTTATGTTACAAACGCCCTTA
1 AATTTAGTGACATTTTATGCCACAAACGCCATTA
* * * * *
13279877 AATTTAATGGCGTTTTATGCCACAAACGTCATTG
1 AATTTAGTGACATTTTATGCCACAAACGCCATTA
*
13279911 AATTTAGCGACATTTT
1 AATTTAGTGACATTTT
13279927 TTAACACAAA
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (34 bp):
AATTTAGTGACATTTTATGCCACAAACGCCATTA
Found at i:13280975 original size:19 final size:19
Alignment explanation
Indices: 13280951--13280999 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
13280941 ATCTCTTATA
13280951 TAAAAACATATGTTATTGT
1 TAAAAACATATGTTATTGT
13280970 TAAAAACATATGTTATTGT
1 TAAAAACATATGTTATTGT
13280989 TAAAAACATAT
1 TAAAAACATAT
13281000 CAACCGTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (19 bp):
TAAAAACATATGTTATTGT
Found at i:13281927 original size:161 final size:159
Alignment explanation
Indices: 13281181--13281953 Score: 531
Period size: 161 Copynumber: 4.8 Consensus size: 159
13281171 CACTTGGGCC
* * * * * *
13281181 TTTCACACATATCAATCC-TAGAAACCAAGTTCAATCATTCGAAAAAGTTGAATATCATATATTG
1 TTTCACACATATCAA-CCGTGGAAACCAAGTTCAATAATTCGGACAAGTTTAATATCATGTATTG
* * * * * ** ** * * *
13281245 AAGCCATCCAAACTGTTAAAATAGATTAATAAAAACAAATTTGTA-CTTTAGCCTTTTAA-AGGC
65 AAACTAT-CAAACTATTAAAACAAAACAATAACTATAAATTTGCATTTTTA-CC-TTTAACA-GC
* ** **
13281308 A-AAAATAGTCTTAAATAGACATAAATGATAACTT
126 ACAAAATA-TCTTAAACAGATGTAAACAATAACTT
* * * ** *
13281342 TTTCATACATATCAACCGTAGAAACCAAGTTCAATCATTCGGACAAACTCAATATCATGTATTGA
1 TTTCACACATATCAACCGTGGAAACCAAGTTCAATAATTCGGACAAGTTTAATATCATGTATTGA
* ** * * * * *
13281407 AACTATCCAACCGTTAAAACATAACAATAA-TATCAAA-TTGTA-TTTTACCTTTTTACAGTA-T
66 AACTATCAAACTATTAAAACAAAACAATAACTAT-AAATTTGCATTTTTACC-TTTAACAGCACA
* * * * *
13281468 AAATGTCTTAAACAAATATAAACATTAGCTT
129 AAATATCTTAAACAGATGTAAACAATAACTT
* * * * **
13281499 TTTCACACATATCAACTGTGGAAGCTAAGTTCAATTATTCCAACAAGTTTAATATCATGTATTGA
1 TTTCACACATATCAACCGTGGAAACCAAGTTCAATAATTCGGACAAGTTTAATATCATGTATTGA
* * * * * * * * * * *
13281564 AGCTATGCAAATTGTTAAAATATAATAATAACAATAAATTTGCATGTTTGCTTCTTAATAGCACA
66 AACTAT-CAAACTATTAAAACAAAACAATAACTATAAATTTGCATTTTTACCT-TTAACAGCACA
*
13281629 AAA-AGTCTTAAACAGATGTAAACGATAACTT
129 AAATA-TCTTAAACAGATGTAAACAATAACTT
* * * * * *
13281660 TTTCACATATATCAACTGTGAAAACCAAATTTAA-ACATTCAGACAAGTTTAATATCATGTATTG
1 TTTCACACATATCAACCGTGGAAACCAAGTTCAATA-ATTCGGACAAGTTTAATATCATGTATTG
* * * *** ** * * *
13281724 GACCTATCCAAACTATTAAAATAAAACAATTTGTCCAAATTTGTATTTTTACCTATTAACGGCAT
65 AAACTAT-CAAACTATTAAAACAAAACAATAACTATAAATTTGCATTTTTACCT-TTAACAGCAC
* * * *
13281789 AAAATATCCTAAATAGATGTAAACAACAATTT
128 AAAATATCTTAAACAGATGTAAACAATAACTT
* * * * * *
13281821 TTTCATACATATCAACCCTGGAAACTAAGGTCAATAATTTGGATAAGTTTAATATCATGTATTGA
1 TTTCACACATATCAACCGTGGAAACCAAGTTCAATAATTCGGACAAGTTTAATATCATGTATTGA
* *
13281886 AACTATCAAAACTATTAAAACAAAACAATAACTATAAATTTGCATTGTTACCTTGTAACGGCACA
66 AACTATC-AAACTATTAAAACAAAACAATAACTATAAATTTGCATTTTTACCTT-TAACAGCACA
13281951 AAA
129 AAA
13281954 AGTTGTAAAC
Statistics
Matches: 478, Mismatches: 119, Indels: 30
0.76 0.19 0.05
Matches are distributed among these distances:
157 78 0.16
158 35 0.07
159 18 0.04
160 35 0.07
161 310 0.65
162 2 0.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (159 bp):
TTTCACACATATCAACCGTGGAAACCAAGTTCAATAATTCGGACAAGTTTAATATCATGTATTGA
AACTATCAAACTATTAAAACAAAACAATAACTATAAATTTGCATTTTTACCTTTAACAGCACAAA
ATATCTTAAACAGATGTAAACAATAACTT
Found at i:13288126 original size:63 final size:61
Alignment explanation
Indices: 13287962--13288296 Score: 233
Period size: 63 Copynumber: 5.3 Consensus size: 61
13287952 CTTTTGAGGG
** * * **
13287962 AATTATTGAAGATATTTTTTGTAGAAAACGCCTTCAATAA-TCACTCCAATTTTTTATCAGGA
1 AATTATTGAAGGCATTTTTTGTAGAAAACGCCTTCAATAATTCACTACAA-TTTTTA-AAAAA
* * * * ** * * *
13288024 GATTATTGAAGGCATATTTTGAATAAAATACCTTTAATAATTCTCTTCAATTTTGTAAAAAA
1 AATTATTGAAGGCATTTTTTGTAGAAAACGCCTTCAATAATTCACTACAATTTT-TAAAAAA
* * * * *
13288086 AATTATTGAAGGTATTTTTTTGTAGAAAACGTCTTCAATAATCCACTGAAAAATTTTAAAAAA
1 AATTATTGAAGGCA-TTTTTTGTAGAAAACGCCTTCAATAATTCACT-ACAATTTTTAAAAAA
* * ** * * *
13288149 ATTTATTGAAGGCATTTTTTTTATAGAAAATACCTTCAATAA-TCAACTAAAACTTTTTATAATA
1 AATTATTGAAGGCA--TTTTTTGTAGAAAACGCCTTCAATAATTC-ACTACAA-TTTTTAAAAAA
* * * * * * *
13288213 AATTATTAAAGGCATTTTTTTTTGTAGAAAACACCTTCAATAATCCATTGAAAATTTTTATAAGA
1 AATTATTGAAGGCA---TTTTTTGTAGAAAACGCCTTCAATAATTCACT-ACAATTTTTAAAAAA
13288278 AATTATTGAAGGCATTTTT
1 AATTATTGAAGGCATTTTT
13288297 AGCCGAAAAT
Statistics
Matches: 217, Mismatches: 46, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
62 54 0.25
63 56 0.26
64 51 0.24
65 51 0.24
66 5 0.02
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (61 bp):
AATTATTGAAGGCATTTTTTGTAGAAAACGCCTTCAATAATTCACTACAATTTTTAAAAAA
Found at i:13288186 original size:64 final size:62
Alignment explanation
Indices: 13288081--13288336 Score: 266
Period size: 65 Copynumber: 4.0 Consensus size: 62
13288071 CAATTTTGTA
* * **
13288081 AAAAAAATTATTGAAGGTATTTTTTTGTAGAAAACGTCTTCAATAATCCACTGAAAAATTTT
1 AAAAAAATTATTGAAGGCATTTTTTTATAGAAAACACCTTCAATAATCCACTGAAAAATTTT
* * *
13288143 AAAAAAATTTATTGAAGGCATTTTTTTTATAGAAAATACCTTCAATAATCAACT-AAAACTTTTT
1 AAAAAAA-TTATTGAAGGCA-TTTTTTTATAGAAAACACCTTCAATAATCCACTGAAAA-ATTTT
* * * * *
13288207 ATAATAAATTATTAAAGGCATTTTTTTTTGTAGAAAACACCTTCAATAATCCATTGAAAATTTTT
1 A-AAAAAATTATTGAAGGCA--TTTTTTTATAGAAAACACCTTCAATAATCCACTGAAAAATTTT
* ** * *
13288272 ATAAGAAATTATTGAAGGCA--TTTTTAGCCGAAAATACCTTCAATAATCCATTGAAAAATTTT
1 A-AAAAAATTATTGAAGGCATTTTTTTA-TAGAAAACACCTTCAATAATCCACTGAAAAATTTT
13288334 AAA
1 AAA
13288337 GGAACTTATT
Statistics
Matches: 167, Mismatches: 20, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
61 7 0.04
62 39 0.23
63 15 0.09
64 44 0.26
65 58 0.35
66 4 0.02
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.38
Consensus pattern (62 bp):
AAAAAAATTATTGAAGGCATTTTTTTATAGAAAACACCTTCAATAATCCACTGAAAAATTTT
Found at i:13288251 original size:65 final size:65
Alignment explanation
Indices: 13287976--13288334 Score: 285
Period size: 62 Copynumber: 5.7 Consensus size: 65
13287966 ATTGAAGATA
* ** * ** *
13287976 TTTTTTGTAGAAAACGCCTTCAATAAT-CACTCCAATTTTTTATCAGGAGATTATTGAAGGCA--
1 TTTTTTGTAGAAAACACCTTCAATAATCCACTGAAAATTTTTAT-AAAAAATTATTGAAGGCATT
13288038 -
65 T
* * * * * * * ** * *
13288038 TATTTTGAATAAAATACCTTTAATAATTCTCT-TCAATTTTGTAAAAAAAATTATTGAAGG--TA
1 TTTTTTGTAGAAAACACCTTCAATAATCCACTGAAAATTTT-TATAAAAAATTATTGAAGGCATT
13288100 T
65 T
** *
13288101 TTTTTTGTAGAAAACGTCTTCAATAATCCACTGAAAAATTTTA-AAAAAATTTATTGAAGGCA-T
1 TTTTTTGTAGAAAACACCTTCAATAATCCACTGAAAATTTTTATAAAAAA-TTATTGAAGGCATT
13288164 T
65 T
* * * * *
13288165 TTTTTTATAGAAAATACCTTCAATAATCAACT-AAAACTTTTTATAATAAATTATTAAAGGCATT
1 TTTTTTGTAGAAAACACCTTCAATAATCCACTGAAAA-TTTTTATAAAAAATTATTGAAGGCATT
13288229 T
65 T
* *
13288230 TTTTTTGTAGAAAACACCTTCAATAATCCATTGAAAATTTTTATAAGAAATTATTGAAGGCA---
1 TTTTTTGTAGAAAACACCTTCAATAATCCACTGAAAATTTTTATAAAAAATTATTGAAGGCATTT
* ** * * *
13288292 TTTTTAGCCGAAAATACCTTCAATAATCCATTGAAAAATTTTA
1 TTTTTTGTAGAAAACACCTTCAATAATCCACTGAAAATTTTTA
13288335 AAGGAACTTA
Statistics
Matches: 238, Mismatches: 46, Indels: 26
0.77 0.15 0.08
Matches are distributed among these distances:
62 83 0.35
63 44 0.18
64 49 0.21
65 58 0.24
66 4 0.02
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (65 bp):
TTTTTTGTAGAAAACACCTTCAATAATCCACTGAAAATTTTTATAAAAAATTATTGAAGGCATTT
Found at i:13288786 original size:297 final size:295
Alignment explanation
Indices: 13288214--13288786 Score: 652
Period size: 297 Copynumber: 1.9 Consensus size: 295
13288204 TTTATAATAA
*
13288214 ATTATTAAAGGCATTTTTTTTTGTAGAAAACACCTTCAATAATCCATTGAAAATTTTTATAAGAA
1 ATTATTAAAGGCATTTTTTTTTGCAGAAAACACCTTCAATAATCCATT-AAAATTTTTATAAGAA
* * *
13288279 ATTATTGAAGGCATTTTTAGCCGAAAATACCTTCAATAATCCATTGAAAAATTTTAAAGGAACTT
65 ATTATTGAAGGCATTTTTAACCAAAAATACCTTCAATAATCCATTGAAAAATTTTAAACGAACTT
* * ** * ** *
13288344 ATTGAATGTGTTTTTCTATAAAAAAAACATTTTCAATAATGATTATTGAATGCATTTTTAGTAAA
130 ATTGAAGGTATTTTTCTAT-AAAAAAACACCTTCAATAATAATTATCAAAAGCATTTTTAGTAAA
* * * * *** *
13288409 AACACCTTCAATAATCAACTAAAAATTTTTAAAGTAATTTATTGAAGGTGTTTTTCTGGTAGAAA
194 AACACCTTCAATAATCAACTAAAAATTTTGAAAGAAAATTATTAAAGGTGTTTTTCTAAAAAAAA
*
13288474 ACACATTCGATAATCTCATCCAATATTTTATTAGGGT
259 ACACATTCAATAATCTCATCCAATATTTTATTAGGGT
* * ** * *
13288511 ATTATTGAAGGCA-TTTTTTTTGCATAAAATGCCTTGAATAATCCCATCT-AATTTTTTATCAAG
1 ATTATTAAAGGCATTTTTTTTTGCAGAAAACACCTTCAATAAT-CCAT-TAAAATTTTTAT-AAG
** * * * * * *
13288574 GTATTATTGAAGGCGTTTTTAATCAAAAATGCTTTCAATTATCCATTGAAAAGTTTTAAACGAAC
63 AAATTATTGAAGGCATTTTTAACCAAAAATACCTTCAATAATCCATTGAAAAATTTTAAACGAAC
* *
13288639 TTATTGAAGGTATTTTT-TAGT-AAGAAACGCCTTCAATAATAATTATCAAAAGCATTTTTAGTT
128 TTATTGAAGGTATTTTTCTA-TAAAAAAACACCTTCAATAATAATTATCAAAAGCATTTTTAG-T
* * *
13288702 AAAAATATCTTCAATAATCCAA-TGAAAATTTTGAAAGAAAATTATTAAAGGTGTTTTTCATAAA
191 AAAAACACCTTCAATAAT-CAACTAAAAATTTTGAAAGAAAATTATTAAAGGTGTTTTTC-TAAA
* *
13288766 AAAAAATACCTTCAATAATCT
254 AAAAAACACATTCAATAATCT
13288787 GCTTTAAAAA
Statistics
Matches: 227, Mismatches: 42, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
295 32 0.14
296 84 0.37
297 110 0.48
298 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (295 bp):
ATTATTAAAGGCATTTTTTTTTGCAGAAAACACCTTCAATAATCCATTAAAATTTTTATAAGAAA
TTATTGAAGGCATTTTTAACCAAAAATACCTTCAATAATCCATTGAAAAATTTTAAACGAACTTA
TTGAAGGTATTTTTCTATAAAAAAACACCTTCAATAATAATTATCAAAAGCATTTTTAGTAAAAA
CACCTTCAATAATCAACTAAAAATTTTGAAAGAAAATTATTAAAGGTGTTTTTCTAAAAAAAAAC
ACATTCAATAATCTCATCCAATATTTTATTAGGGT
Found at i:13299047 original size:47 final size:47
Alignment explanation
Indices: 13298978--13299071 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 47
13298968 TGTTGCTATT
* * * *
13298978 AGTTTGTGTTTATGGACTATTATGGATTGCTAGTGTTAGATAAATTA
1 AGTTTCTGTTTATGGACTATTATGGACTACTAGTGCTAGATAAATTA
13299025 AGTTTCTGTTTATGGACTATTATGGACTACTAGTGCTAGATAAATTA
1 AGTTTCTGTTTATGGACTATTATGGACTACTAGTGCTAGATAAATTA
13299072 TGGACTATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (47 bp):
AGTTTCTGTTTATGGACTATTATGGACTACTAGTGCTAGATAAATTA
Found at i:13299785 original size:16 final size:16
Alignment explanation
Indices: 13299739--13299788 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
13299729 TTATTAAAAG
13299739 AAAATTTTTAAAA--A
1 AAAATTTTTAAAATTA
*** *
13299753 AAAATTCAGAAATTTA
1 AAAATTTTTAAAATTA
13299769 AAAATTTTTAAAATTA
1 AAAATTTTTAAAATTA
13299785 AAAA
1 AAAA
13299789 AACCTCAAAT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
14 9 0.35
16 17 0.65
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (16 bp):
AAAATTTTTAAAATTA
Found at i:13300064 original size:18 final size:19
Alignment explanation
Indices: 13300038--13300088 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
13300028 TTAAAATTAA
* *
13300038 AAAAATAAAAATATTT-TT
1 AAAATTAAAAATATTTCAT
*
13300056 AAAATTAAAAAAATTTCAT
1 AAAATTAAAAATATTTCAT
13300075 AAAACTTAAAAATA
1 AAAA-TTAAAAATA
13300089 GTTAAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 14 0.52
19 5 0.19
20 8 0.30
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAATTAAAAATATTTCAT
Found at i:13300222 original size:19 final size:19
Alignment explanation
Indices: 13300180--13300228 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
13300170 TACAATTTTA
*
13300180 TTTTTATATTTTTTTGAAT
1 TTTTTAAATTTTTTTGAAT
*
13300199 TTTTTAAA-TTTTTTGTATT
1 TTTTTAAATTTTTTTG-AAT
13300218 TTTTTAAATTT
1 TTTTTAAATTT
13300229 AAGTTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 7 0.27
19 17 0.65
20 2 0.08
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.73
Consensus pattern (19 bp):
TTTTTAAATTTTTTTGAAT
Found at i:13300354 original size:20 final size:19
Alignment explanation
Indices: 13300304--13300358 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
13300294 ATTATTTGAT
*
13300304 TTTTCAAAAAATTTTAAAAA
1 TTTTC-AAAATTTTTAAAAA
***
13300324 TTTTTGGAATTCTTTAAAAA
1 TTTTCAAAATT-TTTAAAAA
13300344 TTTTCAAAATTTTTA
1 TTTTCAAAATTTTTA
13300359 TAATATTTAA
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (19 bp):
TTTTCAAAATTTTTAAAAA
Found at i:13300547 original size:28 final size:26
Alignment explanation
Indices: 13300516--13300570 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 26
13300506 TTTAACATTA
13300516 TCATACTTTTTATAATTTT-AAAAATATT
1 TCATA-TTTTTA-AATTTTGAAAAA-ATT
*
13300544 TCATATTTTTAATTTTTGAAAAAATT
1 TCATATTTTTAAATTTTGAAAAAATT
13300570 T
1 T
13300571 TAACAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 9 0.36
27 11 0.44
28 5 0.20
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (26 bp):
TCATATTTTTAAATTTTGAAAAAATT
Found at i:13300763 original size:28 final size:26
Alignment explanation
Indices: 13300732--13300812 Score: 63
Period size: 28 Copynumber: 2.9 Consensus size: 26
13300722 AGTTTTAAAC
*
13300732 TTTTTTAAAATTTTAAAATTTAAAGAA
1 TTTTTCAAAATTTTAAAATTTAAAG-A
* **
13300759 TTTTTCATAAATTTGAAAATTTTTTAGA
1 TTTTTCA-AAATTTTAAAA-TTTAAAGA
* *
13300787 TTATTTTGAAATTTTTAAAATTTAAA
1 -T-TTTTCAAAATTTTAAAATTTAAA
13300813 AAAAAAATTC
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
27 6 0.15
28 15 0.37
29 15 0.37
30 5 0.12
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (26 bp):
TTTTTCAAAATTTTAAAATTTAAAGA
Found at i:13300880 original size:31 final size:29
Alignment explanation
Indices: 13300845--13300920 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 29
13300835 AATTTTAAAA
* *
13300845 AATTTTCTATTATTTTTGTGAAAGTTTTTTG
1 AATTTTCTATTATTTTTAT-AAA-TTTTTGG
* *
13300876 AATTTTCAAATAATTTTTATAAATTTTTGG
1 AATTTTC-TATTATTTTTATAAATTTTTGG
*
13300906 AAGTTTCTATT-TTTT
1 AATTTTCTATTATTTT
13300921 AAGATTTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
28 4 0.11
29 2 0.05
30 12 0.32
31 10 0.27
32 9 0.24
ACGTcount: A:0.28, C:0.04, G:0.09, T:0.59
Consensus pattern (29 bp):
AATTTTCTATTATTTTTATAAATTTTTGG
Found at i:13300902 original size:42 final size:41
Alignment explanation
Indices: 13300823--13300911 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 41
13300813 AAAAAAATTC
*
13300823 AAAGTTTTTTAGAATTTTAAAAAATTTTCTATTATTTTTGTG
1 AAAGTTTTTTAGAATTTTAAAAAATTTTCTATAATTTTTG-G
*
13300865 AAAGTTTTTT-GAATTTTCAAATAATTTT-TATAAATTTTTGG
1 AAAGTTTTTTAGAATTTT-AAAAAATTTTCTAT-AATTTTTGG
13300906 -AAGTTT
1 AAAGTTT
13300912 CTATTTTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
40 6 0.14
41 11 0.26
42 26 0.60
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (41 bp):
AAAGTTTTTTAGAATTTTAAAAAATTTTCTATAATTTTTGG
Found at i:13300929 original size:10 final size:10
Alignment explanation
Indices: 13300913--13300966 Score: 54
Period size: 11 Copynumber: 5.0 Consensus size: 10
13300903 TGGAAGTTTC
13300913 TATTTTTTAA
1 TATTTTTTAA
*
13300923 GATTTTTTAA
1 TATTTTTTAA
*
13300933 TTAATTTTTAA
1 -TATTTTTTAA
13300944 TATTTTTTTAAA
1 TA-TTTTTT-AA
13300956 TAGTTTTTTAA
1 TA-TTTTTTAA
13300967 GTTTTCTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
10 11 0.31
11 15 0.42
12 10 0.28
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (10 bp):
TATTTTTTAA
Found at i:13300950 original size:22 final size:21
Alignment explanation
Indices: 13300916--13300971 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
13300906 AAGTTTCTAT
*
13300916 TTTTTAAGATTTTTTAATTAA
1 TTTTTAAGATTTTTTAAATAA
* *
13300937 TTTTTAATATTTTTTTAAATAGT
1 TTTTTAAGA-TTTTTTAAATA-A
13300960 TTTTTAAG-TTTT
1 TTTTTAAGATTTT
13300972 CTTTTTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 12 0.41
22 10 0.34
23 7 0.24
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (21 bp):
TTTTTAAGATTTTTTAAATAA
Found at i:13301193 original size:23 final size:23
Alignment explanation
Indices: 13301166--13301215 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
13301156 GTTCAAATTA
13301166 ATTTGAGTTTGTGTGATTTTTAC
1 ATTTGAGTTTGTGTGATTTTTAC
13301189 ATTTGAGTTTGTGTGATTTTTAC
1 ATTTGAGTTTGTGTGATTTTTAC
13301212 ATTT
1 ATTT
13301216 CATTTAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.18, C:0.04, G:0.20, T:0.58
Consensus pattern (23 bp):
ATTTGAGTTTGTGTGATTTTTAC
Found at i:13302567 original size:60 final size:58
Alignment explanation
Indices: 13302443--13302939 Score: 524
Period size: 60 Copynumber: 8.4 Consensus size: 58
13302433 TTGTGCAGGG
* * * *
13302443 AAAATTAATACTTTCAATTTTTTTTCAAAAATATTCTTTTGAAATTTTAATTTCGAAG-
1 AAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTTGAAATTTTATTTTC-AAGA
* *
13302501 AAAATTGATACTTTCAACTTTTTTTTAAAAATATTTTTTTGAAAATTTTTATTTTCAACA
1 AAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTTG-AAA-TTTTATTTTCAAGA
* * * * *
13302561 AAAATTGATACTTTTAA-TTTTTCCTCAAAAAT-TGATTTTTGGAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTT-TTCAAAAATAT--TTTTTTGAAA-TTTTATTTTCAAGA
** * *
13302621 AAAATTGATACTTTCAACTTTTCCTCAAAAAATTTTTTTTTGAAATTTTATTTTTAA-A
1 AAAATTGATACTTTCAACTTTTTTTC-AAAAATATTTTTTTGAAATTTTATTTTCAAGA
* *
13302679 GAAAATTGATACTTTTAA-TTTTTCTTCAAAAACTTTCTTTTTTTTGAAATTTT-TTTT-AAGA
1 -AAAATTGATACTTTCAACTTTTT-TTCAAAAA---T-ATTTTTTTGAAATTTTATTTTCAAGA
* * * *
13302740 AAAATTGATACTTTCAACTTTTCTTCAAAAATATTTTTTTGAAAACTTTGATTTTCGAGG
1 AAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTTG-AAA-TTTTATTTTCAAGA
* * * *
13302800 AAAATTGATATTTTCAACCTTTCTTCAAAAA-ATTTTTTTGAAATTTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTTGAAATTTTATTTTCAAGA
* * *
13302857 AAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTTGGAAACTTTGATTTTCAAGA
1 AAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTT-GAAA-TTTTATTTTCAAGA
13302917 AAAATTGATACTTTCAACTTTTT
1 AAAATTGATACTTTCAACTTTTT
13302940 CCTTAAAAAT
Statistics
Matches: 374, Mismatches: 41, Indels: 46
0.81 0.09 0.10
Matches are distributed among these distances:
56 8 0.02
57 42 0.11
58 60 0.16
59 56 0.15
60 165 0.44
61 26 0.07
62 17 0.05
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.48
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTTGAAATTTTATTTTCAAGA
Done.